Do Streptomyces sp. Help Mycorrhization in Raspberry?

Actinobacteria may help the mycorrhizal symbiosis by producing various bioactive metabolites. Mycorrhizae, in turn, are very important since they increase the absorption of nutrients, promoting the growth of their host plant and making inoculation with arbuscular mycorrhizae fungi (AM) a common practice applied in agriculture and forestry. The cultivation of Rubus idaeus (raspberry) is widespread in Patagonia, Argentina; however, the potential benefits of using actinobacteria-mycorrhizal inoculums to enhance crop growth and yield remain unexplored. The objective of this work was to study the interaction between actinobacteria (Streptomyces, Actinomycetota) and AM in raspberry plants. We performed an experiment applying 4 treatments to raspberry plants growing in two substrates, sterile soil and natural (non-sterile) soil. The treatments consisted in a control (without inoculation) and three inoculations treatments (AM, Streptomyces SH9 strain, and AM + Streptomyces). After 3 months of inoculation, mycorrhization parameters (%) and plant growth were recorded. When comparing both substrates, the mycorrhization parameters were higher in natural soil than in sterile soil. The co-inoculation with AM + Streptomyces SH9 showed the highest mycorrhization. Both factors (treatment x substrate) interacted showing that in sterile soil the treatments with the highest effect on mycorrhization parameters were AM and the co-inoculation, while in natural soil all inoculations improved mycorrhization parameters, being highest with the co-inoculation. These results show that Streptomyces SH9 strain helps the mycorrhizal symbiosis in raspberry, being the first report about the effect of a native rhizospheric actinobacterium on an economically important species, promising potential for environmentally friendly improvements in raspberry crops within the temperate Southern Patagonian region.

Biotechnological potential in agriculture of soil Antarctic microorganisms revealed by omics approach.

The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest.

Plant growth promoting bacteria promote rice growth cultivated in two different sandy soils subjected distinct climates conditions.

Sandy soils contain around 70% sand in their composition, making them highly fragile and susceptible to land degradation. Practices such as no-tillage cultivation, the use of bioinoculants, and the application of organic amendments can restore the organic matter in these soils, ensuring sustainable production. In this context, this work aimed to study the microbiological aspects of two sandy soil areas (Brazilian Northeast and South) under contrasting climatic conditions (tropical and temperate). With this purpose, prokaryotic communities were evaluated, and the plant growth-promoting potential of isolated bacteria was assessed by rice inoculation in sandy soil. Despite the high sand content in both soils, soil from the NE was related to the highest phosphorous, calcium, potassium, copper, sodium, zinc, magnesium, and manganese contents, organic matter percentage, and pH. The Shannon diversity index indicated that prokaryotic communities in NE were more diverse than in SU, and PCA revealed that microbial composition exhibited distinct patterns. The rice inoculation experiments were executed to verify if the bacterial isolates displayed a similar growth promotion potential when inoculated in sandy soil areas subjected to different climatic conditions. When all PGP characteristics evaluated were pooled in a PCA, a similar pattern was observed for SU and NE. Burkholderia sp. SU94 was related to highest PGP characteristics evaluated. Paraburkholderia sp. NE32 showed similar results to those of the non-inoculated control. This similar effect of rice growth in the Northeast and South of Brazil suggests that isolate SU94 adapts to different environmental conditions.

Rhodococcus navarretei sp. nov. and Pseudarthrobacter quantipunctorum sp. nov., two novel species with the ability to biosynthesize fluorescent nanoparticles, isolated from soil samples at Union Glacier, Antarctica.

Two Gram-stain-positive bacterial strains, EXRC-4A-4T and RC-2-3T, were isolated from soil samples collected at Union Glacier, Antarctica. Based on 16S rRNA gene sequence similarity, strain EXRC-4A-4T was identified as belonging to the genus Rhodococcus, and strain RC-2-3T to the genus Pseudarthrobacter. Further genomic analyses, including average nucleotide identity and digital DNA-DNA hybridization, suggested that these strains represent new species. Strain EXRC-4A-4T exhibited growth at temperatures ranging from 4 to 28 °C (optimum between 20 and 28 °C), at pH 5.0-9.0 (optimum, pH 6.0), and in the presence of 0-5.0% NaCl (optimum between 0 and 1% NaCl). Strain RC-2-3T grew at 4-28 °C (optimum growth at 28 °C), pH 6.0-10 (optimum, pH 7.0) and in the presence of 0-5.0% NaCl (optimum, 1% NaCl). The fatty acid profile of EXRC-4A-4T was dominated by C17:1 ω-7, while that of RC-2-3T was dominated by anteiso-C15 : 0. The draft genome sequences revealed a DNA G+C content of 64.6 mol% for EXRC-4A-4T and 65.8 mol% for RC-2-3T. Based on this polyphasic study, EXRC-4A-4T and RC-2-3T represent two novel species within the genera Rhodococcus and Pseudarthrobacter, respectively. We propose the names Rhodococcus navarretei sp. nov. and Pseudarthrobacter quantipunctorum sp. nov. The type strains are Rhodococcus navarretei EXRC-4A-4T and Pseudarthrobacter quantipunctorum RC-2-3T. These strains have been deposited deposited in the CChRGM and BCCM/LMG culture collections with entry numbers RGM 3539/LMG 33621 and RGM 3538/LMG 33620, respectively.

Occurrence and diversity of arbuscular mycorrhizal fungi in yerba mate (Ilex paraguariensis - Aquifoliaceae) cultivation environments.

Yerba mate (Ilex paraguariensis) represents a culture of economic, social, and ecological importance for the cultivation regions. Due to the chemical, physical, and biological variations that occur in the different soils where yerba mate is economically exploited, the symbiotic associations with arbuscular mycorrhizal fungi (AMF) guarantee the plant's ability to absorb nutrients. The purpose of this study was to identify and quantify the occurrence of arbuscular mycorrhizal fungi in different environments of yerba mate cultivation. The research was performed in four areas located in the rural area of the municipality of Seberi/RS: Environment with production of yerba mate in the conventional system, silvopastoral system, organic system, and native forest. The normality of residuals and homogeneity of variances assumptions were verified using the Lilliefors and Chi-square tests and the averages compared by the Tukey's test at 5% probability of error. In addition to calculations of diversity, equivalent species, and evenness indices. The presence of AMF spores showed a direct relationship with the phosphorus (P) availability in each treatment, with a count reduction in the organic system, with P content lower than 3 mg kg-1 of soil. The species with the highest predominance were the Acaulosporaceae (Acaulospora colombiana, A. delicata, and A. tuberculata), followed by the Glomaceae (Glomus ambisporum and Glomus pansihalos) in the conventional and silvopastoral systems. The silvopastoral and conventional systems showed the highest levels of Shannon-Weaver diversity (H') and Pielou's evenness, demonstrating greater diversity and consequently greater richness and uniformity.

Isolation and identification of plant growth-promoting rhizobacteria from Spinifex littoreus in Parangkusumo Coastal Sand Dunes, Indonesia.

Utilizing coastal land for agriculture presents challenges such as low water content, high soil salinity, and low organic compound content. To support plant growth under these conditions, biofertilizers composed of plant growth promoting Rhizobacteria (PGPR), especially those inhabiting coastal areas, are needed. The Parangkusumo sand dunes on the southern coast of Java, Indonesia, is a unique coastal ecosystem characterized by arid conditions, high temperatures, and high soil salinity. To date, no studies have reported the isolation of PGPR from this ecosystem. This study is the first to isolate and identify PGPR associated with Spinifex littoreus, a dominant plant species in the Parangkusumo sand dunes, which are adapted to the harsh condition of Parangkusumo sand dunes. Ten rhizobacterial isolates were obtained, with five identified as members of the Bacillaceae family. All isolates demonstrated phosphate solubilization activity, while seven exhibited cellulolytic activity. One isolate, Priestia aryabhattai strain 2, notably showed phosphate solubilization and nitrogen fixation activities. The findings of this PGPR activity screening offer valuable insights for developing biofertilizers tailored for coastal agricultural applications.

Micro PIXE mapping proves a differential distribution and concentration of trace elements in fungal structures of Rhizophagus intraradices.

Arbuscular mycorrhizal (AM) fungi can sequester different potentially toxic elements, such as trace elements (TEs), within their structures to alleviate the toxicity for its host plant and themselves. To elucidate the role of AM fungi in TEs immobilization in the rhizosphere of host plants, it is important to know the TEs distribution in AM fungal structures. In the present study, we investigated the distribution and concentration of TEs within extraradical spores and mycelium of the AM fungus Rhizophagus intraradices, collected from the rhizosphere of Senecio bonariensis plants grown in a soil polluted with multiple TEs, by using Particle-Induced X-ray Emission with a micro-focused beam (micro PIXE). This technique enabled the simultaneous micrometric mapping of elements in a sample. The calculated values were compared with those in the polluted substrate, measured by the Wavelength Dispersive X-ray Fluorescence technique. The highest concentrations of Fe, P, Ti, Mn, Cr, Cu and Zn were found in AM fungal spores, where they were accumulated, while extraradical mycelium was enriched in Cu. Finally, we demonstrated that AM fungi can simultaneously accumulate high amounts of different TEs in their structures, thus reducing the toxicity of these elements to its host plant.

Prevalence of azole-resistant Aspergillus fumigatus and other aspergilli in the environment from Argentina.

Azole resistance has emerged as a new therapeutic challenge in patients with aspergillosis. Various resistance mutations are attributed to the widespread use of triazole-based fungicides in agriculture. This study explored the prevalence of azole-resistant Aspergillus fumigatus (ARAF) and other aspergilli in the Argentine environment. A collection of A. fumigatus and other aspergilli strains isolated from soil of growing crops, compost, corn, different animal feedstuffs, and soybean and chickpea seeds were screened for azole resistance. No ARAF was detected in any of the environmental samples studied. However, five A. flavus, one A. ostianus, one A. niger and one A. tamarii recovered from soybean and chickpea seeds showed reduced susceptibility to medical azole antifungals (MAA). The susceptibility profiles of five A. flavus isolates, showing reduced susceptibility to demethylase inhibitors (DMIs), were compared with those of 10 isolates that exhibited susceptibility to MAA. Aspergillus flavus isolates that showed reduced MAA susceptibility exhibited different susceptibility profiles to DMIs. Prothioconazole and tebuconazole were the only DMIs significantly less active against isolates with reduced susceptibility to MAA. Although no ARAF isolates were found in the samples analysed, other aspergilli with reduced susceptibility profile to MAA being also important human pathogens causing allergic, chronic and invasive aspergillosis, are present in the environment in Argentina. Although a definitive link between triazole-based fungicide use and isolation of azole-resistant human pathogenic aspergilli from agricultural fields in Argentina remains elusive, this study unequivocally highlights the magnitude of the environmental spread of azole resistance among other Aspergillus species.

This study intended to inform about the prevalence of Aspergillus species showing triazole resistance in the Argentinian environment. Since azole fungicides are used for crop protection, it was expected that azole resistance in this species with cross-resistance to medical azoles could occur.

Reassessing the distribution of Burkholderia pseudomallei outside known endemic areas using animal serological screening combined with environmental surveys: The case of Les Saintes (Guadeloupe) and French Guiana.

BACKGROUND: Melioidosis, an emerging infectious disease that affects both humans and animals, is caused by the soil-dwelling bacterium Burkholderia pseudomallei. It is endemic in South and Southeast Asia, and northern Australia, causing an estimated 165,000 human cases annually worldwide. Human cases have been reported in the French West Indies (Martinique and Guadeloupe) since the 1990s. Conversely, no human cases have been reported in French Guiana, a French territory in South America. Our study aimed to investigate whether B. pseudomallei is locally established in Guadeloupe and French Guiana using animals as a proxy. METHODOLOGY/PRINCIPAL FINDINGS: Blood samples were collected from different animals from 56 farms in French Guiana (n = 670) and from two goat farms in Les Saintes (n = 31), part of the Guadeloupe archipelago and tested by enzyme-linked immunosorbent assay (ELISA). In Les Saintes, a serological follow-up was performed, and soil, water and goat rectal swabs were collected and analyzed by culture and PCR. The highest seroprevalence rates (39%) were observed in goats in Les Saintes, followed by horses (24%) and cattle (16%) in French Guiana. In the two goat farms, supplementary analyses detected B. pseudomallei from one goat rectal swab, and a B. pseudomallei strain was isolated from the soil. CONCLUSIONS/SIGNIFICANCE: Our animal serological data suggest the presence of B. pseudomallei in Les Saintes and French Guiana. In Les Saintes, environmental surveys confirmed the endemicity of the bacteria, which is consistent with documented human cases of melioidosis on the island. We did not conduct an environmental survey in French Guiana. Nevertheless, our serological results call for local environmental surveys and a retrospective reassessment of human infections with melioidosis-like symptoms.

Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity.

Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.

Convergence of mcr-1 and broad-spectrum ß-lactamase genes in Escherichia coli strains from the environmental sector.

The mcr-type gene encodes the main plasmid-mediated mechanism of colistin resistance and has been reported in several bacterial species obtained from different sources. Anthropogenic activities in the environment favor the evolution of antimicrobial resistance. Indeed, mcr-1-positive Escherichia coli strains were susceptible to non-polymyxins antimicrobials, but now emerging as multidrug-resistant (MDR) lineages. In this regard, hundreds of surface water and agricultural soil samples were screened for the presence of E. coli carrying the mcr-type genes and mcr-1-positive strains were subjected to in-depth genomic analysis. Almost all colistin-resistant strains were classified as MDR, highlighting those obtained from soils that showed resistance to extended-spectrum cephalosporins and carbapenems. International and high-risk clones of E. coli were identified, with ST10 and ST1720 shared between water and soil samples. Resistome analysis showed a broad resistome (AMR, metal tolerance, and biocide resistance). The mcr-1.1 and mcr-1.26 allelic variants were detected on IncX4 and IncI2 plasmids. Curiously, mcr-1-positive E. coli strains from agricultural soils harbored plasmid-mediated blaCTX-M-1, blaCTX-M-8, or blaKPC-2 genes. Virulome analysis demonstrated traits of a high putative virulence potential, with the presence of extraintestinal pathogenic E. coli. Comparative analysis revealed the persistence and dissemination of plasmid-mediated antimicrobial resistance genes in genetically diversity E. coli strains at the human-animal-environmental interface. These findings demonstrate a possible emerging AMR trend with the convergence of resistance to colistin and broad-spectrum ß-lactams in environmental-derived E. coli strains.

Anaerobic digestates in agricultural soils: A systematic review of their effects on antibiotic resistance genes.

Tackling the dissemination of antibiotic resistance is one of the main global challenges. Manures from animal production are a recognized source of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) requiring appropriate treatment methods. One of the main approaches for manure treatment is anaerobic digestion (AD). Meta-analyses have demonstrated that AD can significantly reduce the load of ARGs. However, antibiotics, ARGs and MGEs still remain in the final product (digestate). A sustainable agricultural use of digestates under the One Health framework requires wide assessments of their effects in the soil resistome. The objective of this review was to present the state of the art of digestate effects on ARGs of agricultural soils, focusing exclusively on digestates from animal manures. A systematic review was conducted. The examination of the resulting literature indicated that although temporal decays are observed for a variety of ARGs in single-application and repeated-applications experiments, for certain ARGs the pre-treatment or control levels are not restored. However, the low number of studies and the heterogeneous experimental conditions preclude a clear understanding of the fate of ARGs in soil and their risk for agroecosystems. The inclusion of multiple MGEs and the assessment of the long-term influence of digestates on soil properties and microbial communities could be keystones for a better understanding of the risks associated with digestate-induced changes in the soil resistome.

Control of inorganic and organic phosphorus molecules on microbial activity, and the stoichiometry of nutrient cycling in soils in an arid, agricultural ecosystem.

Background: The dynamics of carbon (C), nitrogen (N), and phosphorus (P) in soils determine their fertility and crop growth in agroecosystems. These dynamics depend on microbial metabolism, which in turn depends on nutrient availability. Farmers typically apply either mineral or organic fertilizers to increase the availability of nutrients in soils. Phosphorus, which usually limits plant growth, is one of the most applied nutrients. Our knowledge is limited regarding how different forms of P impact the ability of microbes in soils to produce the enzymes required to release nutrients, such as C, N and P from different substrates. Methods: In this study, we used the arable layer of a calcareous soil obtained from an alfalfa cropland in Cuatro Cienegas, México, to perform an incubation experiment, where five different phosphate molecules were added as treatments substrates: three organic molecules (RNA, adenine monophosphate (AMP) and phytate) and two inorganic molecules (calcium phosphate and ammonium phosphate). Controls did not receive added phosphorus. We measured nutrient dynamics and soil microbial activity after 19 days of incubation. Results: Different P molecules affected potential microbial C mineralization (CO2-C) and enzyme activities, specifically in the organic treatments. P remained immobilized in the microbial biomass (Pmic) regardless of the source of P, suggesting that soil microorganisms were limited by phosphorus. Higher mineralization rates in soil amended with organic P compounds depleted dissolved organic carbon and increased nitrification. The C:N:P stoichiometry of the microbial biomass implied a change in the microbial community which affected the carbon use efficiency (CUE), threshold elemental ratio (TER), and homeostasis. Conclusion: Different organic and inorganic sources of P affect soil microbial community structure and metabolism. This modifies the dynamics of soil C, N and P. These results highlight the importance of considering the composition of organic matter and phosphate compounds used in agriculture since their impact on the microbial activity of the soil can also affect plant productivity.

Agricultural Biotechnological Potential of Bacillus velezensis C3-3 and Cytobacillus sp. T106 from Resource Islands of a Semi-arid Zone of La Guajira-Colombia.

Resource islands are vegetative formations in arid and semi-arid ecosystems that harbor microorganisms facing extreme conditions. However, there is a limitation in the knowledge of the agricultural biotechnological potential of microorganisms present in these islands. This study aimed to determine the capacity of Bacillus velezensis C3-3 and Cytobacillus sp. T106 isolates from resource islands to promote plant growth and control the phytopathogen Rhizoctonia solani. The bacteria were sequenced, and both grew at 50 °C, resisted 5% NaCl, withstood UV exposure, and grew in extreme pH conditions. Sixty-six genes in C3-3 and 71 in T106 were identified associated with plant growth promotion, and C3-3 was shown to promote leaf growth in lettuce plants. This promotional effect was associated with the production of indole-3-acetic acid (IAA), phosphorus solubilization, and the presence of genes related to the assimilation of rhizosphere exudates. Both strains inhibited R. solani through the production of volatile compounds and antagonism. Forty-five and 40 of these genes in C3-3 and T106, respectively, were associated with the production of proteases, lipases, siderophores, antimicrobial compounds, degradation enzymes, and secretion systems. Notably, Cytobacillus sp. has not been previously reported as a biocontrol agent. This work contributes to the evidence of the biotechnological potential of semi-arid region bacteria, offering prospects for improving agricultural production in areas with limiting conditions.

Production and biochemical and biophysical characterization of fibrinolytic protease of a Mucor subtilissimus strain isolated from the caatinga biome.

Cardiovascular diseases, resulting from the deposition of clots in blood vessels, are the leading cause of death worldwide. Fibrinolytic enzymatic activity can catalyze blood clot degradation. Findings show that 36 fungal isolates recovered from Caatinga soils have the potential to produce fibrinolytic protease under submerged conditions. About 58 % of the isolates displayed fibrinolytic activity above 100 U/mL, with Mucor subtilissimus UCP 1262 being the most active. The protease was biochemically and biophysically characterized, showing that the enzyme had a high affinity for SAApNA substrate and was significantly inhibited by fluoride methyl phenyl sulfonyl-C7H7FO2S, suggesting that it is a chymotrypsin-like serine protease. The highest enzyme activity was detected at pH 5.0 and 28 °C. This fibrinolytic protease's far-UV circular dichroism (CD) showed that its secondary structure was primarily α-helical. The purified fibrinolytic enzyme may represent a novel therapeutic agent for treating thrombosis. At temperatures above 65 °C, the enzyme lost all its secondary structure. Its melting temperature was 58.1 °C, the denaturation enthalpy 85.1 kcal/mol, and the denaturation entropy 0.26 kcal/K∙mol.

Metagenomics and vegetative growth of Salvia hispanica inoculated with Trichoderma harzianum.

The soil is a dynamic environment, influenced by abiotic and biotic factors, which can result in changes in plant development. This study aimed to assess the impact on vegetative growth of chia (Salvia hispanica L) inoculated with Trichoderma harzianum and on the rhizosphere microbiome. The experimentation was conducted in a greenhouse under controlled conditions growing chia plants in pots containing soil with a clayey texture. Different concentrations of T. harzianum (0; 2.5; 5.0; 10.0; 20.0 µL. g-1 of seed) were applied to the chia seeds before planting. Morphological parameters, including plant height (cm), number of branches, stem diameter (mm), number of days to flowering and shoot and root dry masses (g) were quantitatively assessed. After the cultivation period, soil samples from the rhizosphere region were collected for subsequent chemical and metagenomic analyses. These samples were also compared with the control soil, collected before installing the experiment. The results showed that increasing doses of T. harzianum promoted a significant increase in the diameter of the stem, number of branches, dry biomass of the root system and the number of days to flowering, without modifying the overall height of the plants. Soil metagenomics indicated that T. harzianum inoculation modified the microbial diversity of the rhizosphere environment, with more pronounced effects observed in samples treated with higher concentrations of the inoculant. Furthermore, there were changes in the chemical composition and enzymes related to soil quality in correlation with the concentrations of the applied inoculant. This study demonstrated that inoculating chia seeds with T. harzianum not only promotes specific morphogenetic characteristics of the plant, but it also has a significant impact on the microbial diversity and biochemical functionality of the soil, including an observed increase in the populations of T. harzianum and T. asperellum.

Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.

BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics. RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria. CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.

The potential use of Pseudomonas in terrestrial and space agriculture.

In the last few years, there has been an increasing interest in solutions for sustainable agriculture to reduce negative impacts on the environment resulting from modern agricultural practices. The use of environmentally beneficial bacteria, like Pseudomonas, which can increase plant productivity by reducing growth time, is a promising opportunity for sustainable agriculture. Pseudomonas is a gram-negative bacterium genus, commonly present in soils, plants, and irrigation water. Pseudomonas has a wide range of metabolic routes that could benefit agriculture, such as nutrient uptake, pathogen suppression, heavy metal solubilization, drought tolerance, and high salt concentration tolerance. Pseudomonas may even be proposed as a potential tool for future agriculture on other planets, where the use of microorganisms would be essential for crop development in hostile and inhospitable environments. Hence, the present review discusses the potential use of Pseudomonas in sustainable agriculture on planet Earth and potentially on Mars, highlighting its role in plant growth enhancement and plant protection from pathogenic microorganisms.

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories.

BACKGROUND: Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation. RESULTS: Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. CONCLUSION: Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.

Environment and microbiome drive different microbial traits and functions in the macroscale soil organic carbon cycle.

Soil microbial traits and functions play a central role in soil organic carbon (SOC) dynamics. However, at the macroscale (regional to global) it is still unresolved whether (i) specific environmental attributes (e.g., climate, geology, soil types) or (ii) microbial community composition drive key microbial traits and functions directly. To address this knowledge gap, we used 33 grassland topsoils (0-10 cm) from a geoclimatic gradient in Chile. First, we incubated the soils for 1 week in favorable standardized conditions and quantified a wide range of soil microbial traits and functions such as microbial biomass carbon (MBC), enzyme kinetics, microbial respiration, growth rates as well as carbon use efficiency (CUE). Second, we characterized climatic and physicochemical properties as well as bacterial and fungal community composition of the soils. We then applied regression analysis to investigate how strongly the measured microbial traits and functions were linked with the environmental setting versus microbial community composition. We show that environmental attributes (predominantly the amount of soil organic matter) determined patterns of MBC along the gradient, which in turn explained microbial respiration and growth rates. However, respiration and growth normalized for MBC (i.e., specific respiration and growth) were more linked to microbial community composition than environmental attributes. Notably, both specific respiration and growth followed distinct trends and were related to different parts of the microbial community, which in turn resulted in strong effects on microbial CUE. We conclude that even at the macroscale, CUE is the result of physiologically decoupled aspects of microbial metabolism, which in turn is partially determined by microbial community composition. The environmental setting and microbial community composition affect different microbial traits and functions, and therefore both factors need to be considered in the context of macroscale SOC dynamics.