Archaea diversity in vegetation gradients from the Brazilian Cerrado

The adaptations of the microbial communities of the savanna soil over a period of wildfire, after the first rains, and during the rainy season

Annually, the Cerrado ecosystem alternates between dry periods and long rainy seasons. During the dry season, severe forest fires occur, consuming a considerable part of the native vegetation, which impacts directly on the microbiome of the soil. Evaluate the adaptations of the soil microbiome to drought, rain and wildfire. Sequencing of the 16S rRNA gene was carried out for three significant conditions: drought and forest fires ("Fire"), after the first recorded rains ("First_Rain"), and during the rainy season ("Rainy"). It has been shown that under the "Fire" condition, there was a predominance of Phylum Actinobacteria, followed by Proteobacteria and Firmicutes. With the advent of the rainy season, "First_Rain," there was a change in the predominant taxonomic groups, with a higher prevalence of members of Proteobacteria and Firmicutes. During the rainy season, Proteobacteria and Firmicutes continued as the most prevalent groups. However, it was noted that in this period, there was an increase in bacterial diversity when compared with other periods analyzed. These results show how environmental factors influence adaptations in microbial communities. This allows for a better understanding of how to link the structure of the microbial community to the performance of ecosystems, and assist in preventing the consequences of increased frequency of wildfires, and long periods of drought.

Effect of low-thermal pretreatment on the methanogenic performance and microbiome population of continuous high-solid anaerobic digester treating dewatered sludge

Undigested and dewatered sludge at 10% total solids was pretreated at 60 °C for 3 h and fed to a lab-scale horizontal anaerobic bioreactor for 130 days with solids retention time (SRTs) from 25 to 16 d. The low-thermal pretreatment enabled higher net energy production, improved sludge treatment efficiency, and enhanced digestion stability. The highest average biomethane yield and production rate were 138.5 mL/g VS and 0.43 L/L.d, respectively, and the economic benefit was expected to be the maximum at SRT 16 d. Pretreatment did not increase the specific methanogenic activity per unit methanogen, but resulted in higher abundance of methanogenic archaea and hydrolytic bacteria. Methanogenic population shifted from hydrogenotrophic to acetoclastic, consistent with predicted gene expression at SRT equal or below 20 d. Anaerobic digestion along with low-thermal could be a feasible management strategy for undigested dewatered sludge from small WWTPs.

The rhizosphere of Salix viminalis plants after a phytostabilization process assisted by biochar, compost, and iron grit: chemical and (micro)-biological analyses

Amendments, such as biochar, compost, and iron grit, used in phytostabilization studies, showed positive effects on soil physico-chemical properties, plant growth, and the microbial community. However, assisted phytostabilization studies do not always focus on the rhizosphere area where soil, plants, and microorganisms are affected by the amendments and plants and microorganisms can also interact with each other. The aims of this study were to evaluate the effects of amendment application on the exudation of organic acids by Salix viminalis plant roots, as well as the effects of amendments and plant development on the soil CHNS contents and the microbial community activity and diversity, assessed by measuring enzyme activities and using Biolog EcoPlates^TM tests and next-generation sequencing analyses. The results of the mesocosm experiment showed that soil C, H, and N contents were increased by amendment application, especially biochar and compost, while the one of S decreased. Enzyme activities, microbial activity, and diversity were also increased by the addition of amendments, except iron grit alone. Finally, the quantity of organic acids exuded by roots were little affected by amendments, which could in part explain the reduced effect of plant development on soil chemical and microbiological parameters. In conclusion, this study showed in particular that biochar and compost were beneficial for the soil CHN contents and the microbial community while affecting poorly Salix viminalis root exudates.

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire

Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.

The profile of the soil microbiota in the Cerrado is influenced by land use

Extensive areas of the Cerrado biome have been deforested by the rapid advance of agricultural frontiers, especially by agricultural monocultures, and cultivated pastures. The objective of this study was to characterize the soil microbial community of an environment without anthropogenic interference and to compare it with soybean soil and pasture areas. For that, metagenomic sequencing techniques of the 16S rRNA gene were employed. Consistent changes in the profiles of diversity and abundance were described between communities in relation to the type of soil. The soil microbiome of the native environment was influenced by the pH level and content of Al³⁺, whereas the soil microbiomes cultivated with soybean and pasture were associated with the levels of nutrients N and P and the ions Ca²⁺ and Mg²⁺, respectively. The analysis of bacterial communities in the soil of the native environment showed a high abundance of members of the Proteobacteria phylum, with emphasis on the Bradyrhizobium and Burkholderia genera. In addition, significant levels of species of the Bacillus genus, and Dyella ginsengisoli, and Edaphobacter aggregans of the Acidobacteria phylum were detected. In the soil community with soybean cultivation, there was a predominance of Proteobacteria, mainly of the Sphingobium and Sphingomonas genera. In the pasture, the soil microbiota was dominated by the Firmicutes, which was almost entirely represented by the Bacillus genus. These results suggest an adaptation of the bacterial community to the soybean and pasture cultivations and will support understanding how environmental and anthropogenic factors shape the soil microbial community. KEY POINTS: • The Cerrado soil microbiota is sensitive to impacts on the biome. • Microbial communities have been altered at all taxonomic levels.

An Actinobacterium Strain From Soil of Cerrado Promotes Phosphorus Solubilization and Plant Growth in Soybean Plants

The huge biological diversity of the Brazilian Cerrado is an important source of economically interesting microbial agents. The phylum Actinobacteria plays an important role in nutrient cycling, potentially improving their availability to plants. In this study, we isolated an actinobacteria (strain 3AS4) from wheat rhizospheres of crops cultivated in the Cerrado biome. Strain 3AS4 was identified as belonging to the genus Streptomyces and had phosphorus mobilization ability, mineralizing approximately 410 μg ml^–1 from phytate, 300 μg ml^–1 from calcium phosphate, and 200 μg ml^–1 from rock phosphate. The analysis of the actinobacteria crude extract by spectrometric techniques revealed the presence of gluconic and 2-ketogluconic acid, and a greenhouse experiment was carried out to evaluate its plant growth promotion activity in soybean. Soil in its natural condition (with no phosphorus addition), 40 kg ha^–1 rock phosphate from Bayovar (RP) added to soil, and triple super phosphate (SPT) added to soil were used. Significant differences in plant height were observed at 6 weeks when the plants were inoculated with the 3AS4 strain. The growth of inoculated plants in natural condition was promoted in 17% compared with the RP and SPT non-inoculated conditions, suggesting that inoculation can enable plants to grow with lower chemical P fertilizers. In the plants that were inoculated with the 3AS4 strain in the RP condition, the plant height increased by approximately 80% and the shoot:root ratio was approximately 30% higher compared to control conditions (non-inoculated plants in natural conditions). 3AS4 has P-solubilizing potential and can be exploited as an inoculant for soybean cultivation. These results suggest that this actinobacterium is a valuable resource for sustainable agriculture and will allow the reduction of phosphate fertilization in the future.

Soil microbial C:N:P ratio across physiognomies of Brazilian Cerrado Soil microbial biomass across a gradient of preserved native Cerrado

Different physiognomies across the Cerrado could influence the microbial C:N:P ratio in the soil since these physiognomies present different abundance and diversity of plant species. Thus, the aim of this study was to evaluate the microbial C:N:P ratio in soil across three different physiognomies of Cerrado in the Northeast, Brazil, namely campo graminóide (dominance of grasses), cerrado stricto sensu (dominance of grasses, shrubs, low trees, and woody stratum), and cerradão (dominance of woody stratum). Campo graminóide was characterized by lower values of total organic C, N, microbial C:P, N:P, and soil C:N. Cerrado stricto sensu presented average values for most of the measured parameters, while cerradão presented higher values of microbial C, N, P, organic C, N and soil C:P and C:N ratios. The principal component analysis showed that the samples grouped according to the sites, with a clear gradient from campo graminóide to cerradão. Therefore, the differences of vegetation across physiognomies of Cerrado influenced the soil microbial C:N:P ratio, where cerradão showed highest microbial C:N:P ratio than soil under campo graminóide.

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 7^th 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.

Araujo et al. investigate the soil microbiome across four major vegetation zones of the Brazilian Cerrado and find that protist taxon richness increases towards the tree-dominated climax vegetation. Their findings suggest that increased microbiome complexity might enhance system stability towards climax vegetation.