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The plant microbiome is one of the most important environments for ecological interactions between bacteria that impact the plant and the ecosystem. However, studies on the diversity of mobile genetic elements (such as plasmids) associated with the plant microbiome are very scarce. Here, we determined the bacterial community composition and the occurrence of plasmids in the microbiota associated with sea fig, Carpobrotus aequilaterus (N.E. Br.), a succulent species widely used as an ornamental plant in Chile. The abundance and composition of the endophytic and rhizospheric bacterial communities were determined by quantitative PCR (qPCR) and DNA metabarcoding analysis. Plasmid diversity in the plant microbiome was determined by plasmid DNA extraction and screened by endpoint PCR of backbone genes for four different incompatibility groups (Inc). The results showed about 106 copies of the 16S rRNA gene in the endosphere and rhizosphere, showing significant differences according to the diversity index. Proteobacteria (Pseudomonadota; 43.4%), Actinobacteria (Actinomycetota; 25.7%), and Bacteroidetes (Bacteroidota; 17.4%) were the most dominant taxa in both plant compartments, and chemoheterotrophy (30%) was the main predicted function assigned to the microbiota. Plasmid diversity analysis showed the presence of transferable plasmids in the endosphere and rhizosphere of C. aequilaterus, particularly among environmental plasmids belonging to the IncP and IncN incompatibility groups. [ABSTRACT FROM AUTHOR]

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs. [ABSTRACT FROM AUTHOR]

Since 2016, crown death and mortality of Araucaria araucana trees have been observed at different localities of the Nahuelbuta Coastal Range, Chile. The objective of this study was to determine the presence of Phytophthora spp. in the rhizosphere of A. araucana trees that may explain its decline. Samples of soil rhizosphere were collected from trees with crown death as well as from asymptomatic trees at two visually contrasting severity areas. Phytophthora detection from soil samples was carried out using leaf bait technique, and isolates were identified by morphology and molecular methods. Recovered Phytophthora isolates were used in pathogenicity tests with A. araucana plants. From rhizosphere soil samples of 30 A. araucana trees, 56 isolates of Phytophthora cinnamomi were obtained. Isolations were more frequent in the rhizosphere of trees with severe crown symptoms and originated exclusively from the selected area showing severe crown symptoms. Plant stem inoculation with P. cinnamomi isolates caused 100% mortality; however, through root infestation, mortality was variable depending on the specific isolate. These results are the first report of the pathogenicity of P.cinnamomi A2 in natural forests of A. araucana in Chile. [ABSTRACT FROM AUTHOR]

The diversity of orchid mycorrhizal fungi (OMF) and other beneficial root-associated fungi in temperate forests has scarcely been examined. This study aimed to analyze the diversity of mycorrhizal and rhizosphere-associated fungal communities in the terrestrial orchids Gavilea lutea and Chloraea collicensis growing in high-orchid-population-density areas in the piedmont of the Andes Cordillera with native forest (Nothofagus-Araucaria) and Coastal Cordillera with an exotic plantation (Pinus-Eucalyptus) in south-central Chile. We focused on rhizosphere-inhabiting and peloton-associated OMF in a native forest (Andes Cordillera) and a mixed forest (Coastal Cordillera). The native terrestrial orchids G. lutea and C. collicensis were localized, mycorrhizal root segments were taken to isolate peloton-associated OMF, and rhizosphere soil was taken to perform the metabarcoding approach. The results revealed that Basidiomycota and Ascomycota were the main rhizosphere-inhabiting fungal phyla, showing significant differences in the composition of fungal communities in both sites. Sebacina was the most-abundant OMF genera in the rhizosphere of G. lutea growing in the native forest soil. In contrast, Thanatephorus was the most abundant mycorrhizal taxa growing in the rhizosphere of orchids from the Coastal Cordillera. Besides, other OMF genera such as Inocybe, Tomentella, and Mycena were detected. The diversity of OMF in pelotons differed, being mainly related to Ceratobasidium sp. and Tulasnella sp. These results provide evidence of differences in OMF from pelotons and the rhizosphere soil in G. lutea growing in the Andes Cordillera and a selection of microbial communities in the rhizosphere of C. collicensis in the Coastal Cordillera. This raises questions about the efficiency of propagation strategies based only on mycorrhizal fungi obtained by culture-dependent methods, especially in orchids that depend on non-culturable taxa for seed germination and plantlet development. [ABSTRACT FROM AUTHOR]

Chilean native forests have been subjected to several types of disturbances, with one of them being the replacement by exotic species. Pinus radiata D. Don is a widespread exotic tree that forms extensive plantations in southern Chile. It covers extended areas, affecting the landscape, biodiversity, and ecosystem services associated with native forest ecosystems. Although advances in assessing the impact of exotic plant species have been conducted, few studies have focused on the alteration of soil microorganisms. This study aimed to characterize the rhizosphere bacterial and fungal communities associated with the tree species Nothofagus obliqua inside a native forest stand and within a P. radiata plantation growing nearby. We used a 16S rRNA gene and ITS region metabarcoding approach. Using bioinformatics, diversity indices, relative abundance, preferential taxa, and predicted functions and guilds were estimated. The β-diversity analysis showed that both factors, the type of soil (rhizosphere or bulk soil) and the type of site (native forest or P. radiata plantation), were significant, with the site explaining most of the variation among bacterial and fungal communities. Proteobacteria and Basidiomycota were the most abundant bacterial and fungal phyla in both types of soil and sites. Similarly, bacteria showed similar abundant taxa at the family level, independent of the soil type or the site. The main fungal taxa associated with native forests were Tricholomataceae and Cantharellales, whereas in P. radiata plantations, Russulaceae and Hyaloscyphaceae were the most abundant families. The main bacteria functional groups were chemoheterotrophy and aerobic chemoheterotrophy, without significant differences between the type of soil or sites. Overall, these results demonstrate that the composition and diversity of bacterial and fungal communities associated with native N. obliqua forest are influenced by the surrounding forest, and mainly depend on the site's characteristics, such as the lignin-rich wood source. These results improve our understanding of the impact of native forest replacement on soil microbial communities, which can alter microbial-related soil ecosystem services. [ABSTRACT FROM AUTHOR]

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou's evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems. [ABSTRACT FROM AUTHOR]

Two novel Micromonospora strains, STR1-7 T and STR1S-6 T , were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora . They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7 T is most closely related to Micromonospora orduensis S2509 T , and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7 T and STR1S-6 T be recognized as representing new species in the genus Micromonospora , namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7 T (=CECT 9665 T =LMG 30768 T ) and STR1S-6 T (=CECT 9666 T =LMG 30770 T ), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.

Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments. [ABSTRACT FROM AUTHOR]

Chile's seedling production industry has been growing for the last 10 years, and demand has actually reached 1250 million seedlings per year. This system has special relevance due to the high cost of seeds. In addition, there is an increasing demand for substituting synthetic agrochemicals. Therefore, the potential use of plant growth-promoting rhizobacteria (PGPR) in tomato production has been investigated. Before sowing, the micro-organisms provided by Biogram S.A. were inoculated into the substrate diluted in 250 mL/L unchlorinated water. The experiment was laid out in a ‘split-plot’ design with the two plant substrates as main plots and the inoculants as subplots, including six replicates per treatment. Tomato seedlings were grown using two different plant substrates: a mixture of 70% peat and 30% perlite by volume, and a substrate with 20% peat, 20% perlite and 60% compost by volume, both inoculated withBacillus subtilisorPseudomonas fluorescensor Bioroot®, which is a commercial product containingB. subtilis,P. fluorescens,Trichoderma harzianum, yeast, algae andNocardia. For control, uninoculated tomato seedlings were grown on the respective plant substrates. Variance analysis did not identify significant interactions between substrate type (main plots) and inoculation treatment (subplots),P≤ 0.05. There were significant differences between inoculants (P≤ 0.05). Means were compared by using the Tukey's multiple range test. Tomato growth in terms of leaf area (cm2/plant) and shoot and root dry weight (g/10 plants) was improved for the seedlings grown on the substrate with 70% peat and 30% perlite, compared to the compost containing an alternative that is valid for both uninoculated perlite peat and all inoculated treatments where perlite peat was outstanding. Inoculation with Bioroot® improved the leaf area, shoot dry weight, root dry weight, radical contact area, volume of roots and root forks compared with the control without inoculation, when both plant substrates were analysed together. Thus, inoculation with Bioroot® can be recommended as an alternative to tomato seedling growers' dependence on synthetic agrochemicals. [ABSTRACT FROM PUBLISHER]

The effect of nitrogen (N) and phosphorus (P) fertilization on composition of rhizobacterial communities of volcanic soils (Andisols) from southern Chile at molecular level is poorly understood. This paper investigates the composition of rhizobacterial communities of two Andisols under pasture after 1- and 6-year applications of N (urea) and P (triple superphosphate). Soil samples were collected from two previously established sites and the composition of rhizobacterial communities was determined by denaturing gradient gel electrophoresis (PCR-DGGE). The difference in the composition and diversity between rhizobacterial communities was assessed by nonmetric multidimensional scaling (MDS) analysis and the Shannon-Wiener index. In Site 1 (fertilized for 1 year), PCR-DGGE targeting 16S rRNA genes and MDS analysis showed that moderate N application (270 kg N ha year) without P significantly changed the composition of rhizobacterial communities. However, no significant community changes were observed with P (240 kg P ha year) and N-P application (270 kg N ha year plus 240 kg P ha year). In Site 2 (fertilized for 6 years with P; 400 kg P ha year), PCR-DGGE targeting rpoB, nifH, amoA and alkaline phosphatase genes and MDS analysis showed changes in rhizobacterial communities only at the highest rate of N application (600 kg N ha year). Quantitative PCR targeting 16S rRNA genes also showed higher abundance of bacteria at higher N application. In samples from both sites, the Shannon-Wiener index did not show significant difference in the diversity of rhizobacterial communities. The changes observed in rhizobacterial communities coincide in N fertilized pastures with lower soil pH and higher pasture yields. This study indicates that N-P application affects the soil bacterial populations at molecular level and needs to be considered when developing fertilizer practices for Chilean pastoral Andisols. [ABSTRACT FROM AUTHOR]

Cereal production in southern Chile is based on ash-derived volcanic Andisols, which present suboptimal levels of available selenium (Se). Strategies are needed to improve Se content in cereal crops and concomitantly improve the nutritional quality of grain. Here, we investigated the occurrence of Se-tolerant bacteria (STB) in Andisols and evaluated Se tolerance and accumulation in STB. The inoculation of wheat with STB and the contributions of these bacteria to Se content in plants were also evaluated under greenhouse conditions. The results showed that Se amendment of Andisols stimulated some bacterial groups ( Paenibacillaceae and Brucellaceae) but inhibited others (Clostridia, Burkholderiales, Chitinophagaceae and Oxalobacteraceae), as revealed by denaturing gradient gel electrophoresis. Furthermore, we found four STB isolates that displayed 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase activity) and that carried the acdS gene as revealed by PCR. The selected STB were characterised as Stenotrophomonas, Bacillus, Enterobacter and Pseudomonas according to partial sequencing of the 16S rRNA gene. After 24 h of culture in nutrient broth, the selected STB showed the ability to grow in high Se concentrations (5 and 10 mM) and to accumulate elemental Se in micro- and nanospherical deposits, transforming 50-80 % of the Se initially added. Greenhouse experiments with wheat showed that Se associated with STB (micro- and nanospheres of elemental Se and other intracellular forms) can be translocated into leaves of wheat plantlets. [ABSTRACT FROM AUTHOR]

Specimens from soil samples collected at Cocalan, Chile, from the rhizosphere of the Chilean wine palm, Jubaea chilensis, were sent to the Plant Protection Institute, Bari, Italy. The identification revealed the presence of large numbers of Paralongidorus sacchari and a few specimens of Paraxiphidorus michelluci, including several juveniles. Populations were studied morphologically and morphometrically and results are reported herein. Both species represent new records for Chile. Juveniles of Paraxiphidorus michelluci are described for the first time. [ABSTRACT FROM AUTHOR]

Plants must deal with harsh environmental conditions when colonizing abandoned copper mine tailings. We hypothesized that the presence of a native microbial community can improve the colonization of the pioneer plant, Baccharis linearis, in soils from copper mining tailings. Plant growth and microbial community compositions and dynamics were determined in cultivation pots containing material from two abandoned copper mining tailings (Huana and Tambillos) and compared with pots containing fresh tailings or surrounding agricultural soil. Controls without plants or using irradiated microbe-free substrates, were also performed. Results indicated that bacteria (Actinobacteria, Gammaproteobacteria, and Firmicutes groups) and fungi (Glomus genus) are associated with B. linearis and may support plant acclimation, since growth parameters decreased in both irradiated (transiently without microbial community) and fresh tailing substrates (with a significantly different microbial community). Consistently, the composition of the bacterial community from abandoned copper mining tailings was more impacted by plant establishment than by differences in the physicochemical properties of the substrates. Bacteria located at B. linearis rhizoplane were clearly the most distinct bacterial community compared with those of fresh tailings, surrounding soil and non-rhizosphere abandoned tailings substrates. Beta diversity analyses showed that the rhizoplane bacterial community changed mainly through species replacement (turnover) than species loss (nestedness). In contrast, location/geographical conditions were more relevant than interaction with the plants, to explain fungal community differences.

Fully mycoheterotrophic plants have attracted attention due to their ability to obtain carbon and mineral nutrients directly from fungal hyphae. However, research on bacteria associated with full mycoheterotrophs is limited. This study identifies rhizosferic and endophytic bacteria associated with A. uniflora rhizomes and analyzes their ability to produce microbial metabolites of various functions. Eight bacterial OTUs were revealed, and their potential roles in plant-growth promotion and antimicrobial activities were demonstrated. These findings suggest that root-system associated bacteria can be considered as essential microorganisms for growth and development of fully mycoheterotrophic plants. • Bacteria associated with Arachnitis uniflora rhizomes were isolated and identified. • Eight bacterial OTUs were isolated from the rhizomes. • Plant growth promoter-metabolites and inhibition of fungal growth were detected. [ABSTRACT FROM AUTHOR]

• Arbuscular mycorrhizal symbiosis is strongly affected by fire in A. araucana forests. • Glomalin-related soil protein was a good indicator of soil stability in unburned areas. • Better performance for A. araucana forests is in the coastal range. • High rates of mycorrhization, fungal structures and enzyme activities were in the coastal range. Araucaria araucana is a long-lived native conifer from the sub-Antarctic Andean forests of South America. Currently, the species is classified as endangered due to fragmentation, deforestation and increasing fire events affecting southern Chile. Although fire is a key factor shaping the dynamics of A. araucana forests, the impact of fire on the chemical and microbiological soil properties remains elusive. Here, we aimed to characterize the (bio)chemical and microbiological soil traits in different sites of the Andes and the Coastal range of southern Chile, as a way to describe the conservation status of A. araucana forests in contrasting environments with different fire history. The study was conducted in old-growth A. araucana forests within protected areas affected by different fire events during the last 18 years. Roots were analyzed for arbuscular mycorrhizal (AM) colonization and soil samples were processed for (bio)chemical and microbiological analyses. Our results revealed that AM colonization was strongly affected by fire, being closely related with the acid phosphatase and β-glucosidase enzymatic activities, which also showed lower values in fire-affected sites. Glomalin-related protein in the soil was also a good indicator of soil stability associated to environments non-affected by fire. Based on our results, the conservation status benchmark for A. araucana is in the Coastal range, showing high rates of AM colonization, fungal structures and biochemical activities in environments subjected to minor geological risks and no fire events. This research provides helpful information for finding efficient biological inoculants, including indigenous AM fungal species, which can help to enhance A. araucana plantlets with an optimized rhizosphere oriented to the restoration of burned A. araucana forests in south-central Chile. [ABSTRACT FROM AUTHOR]

The bacterial strain M7D1 T was isolated from samples of the rhizosphere of desert bloom plants on the Atacama region located in northern Chile as part of a study intended to isolate nitrifying bacteria in this adverse environment. It was previously identified as belonging to the Pseudomonas fluorescens group. In this study, the phylogenetic analysis of the 16s RNA, gyrA, rpoB and rpoD genes confirmed that this strain belongs to this group, especially Sub Group (SG) Koreensis, but it represents a potential new species. Additionally, the average nucleotide identity confirmed this as the highest identity value (0.92) with Pseudomonas moraviensis LMG 24280, which is lower than the 0.94 threshold established to classify two strains within the same species. The strain M7D1 T shared a similar fatty acids methyl ester profile than the type strains of other Pseudomonas spp. previously described. Furthermore, it can be differentiated phenotypically from other related species of SG P. koreensis. Based on these results, the existence of a new species of Pseudomonas is demonstrated, for which the name Pseudomonas atacamensis is proposed. This strain presented a set of genes associated with plant growth-promoting rhizobacteria and it is a good candidate to be used for recovery of contaminated soils. However, more studies are required to demonstrate whether this bacterium is non-pathogenic, can survive in the presence of toxic compounds and promote growth or help to the stress management of plants.

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.

Phytate is one of the most abundant sources of organic phosphorus (P) in soils, but must be mineralized by phytase-producing bacteria to release P for plant uptake. Microbial inoculants based on Bacillus spp. have been developed commercially, but few studies have evaluated the ecology of these bacteria in the rhizosphere or the types of enzymes that they produce. Here, we studied the diversity of aerobic endospore-forming bacteria (EFB) with the ability to mineralize phytate in the rhizosphere of pasture plants grown in volcanic soils of southern Chile. PCR methods were used to detect candidate phytase-encoding genes and to identify EFB bacteria that carry these genes. This study revealed that the phytate-degrading EFB populations of pasture plants included species of Paenibacillus and Bacillus, which carried genes encoding β-propeller phytase (BPP). Assays of enzymatic activity confirmed the ability of these rhizosphere isolates to degrade phytate. The phytase-encoding genes described here may prove valuable as molecular markers to evaluate the role of EFB in organic P mobilization in the rhizosphere., (© 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)