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The use of high-throughput DNA sequencing (HTS) has revealed the great diversity of rhizobacteria in plant rhizospheres; however, only a minor portion (≤ 1%) of rhizobacteria belonging to few taxa can be cultured under laboratory conditions. In recent years, in situ cultivation has opened a window to explore a greater diversity of bacterial taxa in the environment. Here, we explored the total and culturable rhizobacterial communities associated with the rhizosphere of wheat plants by using 16S rRNA-based HTS and in situ cultivation with microwell chambers (MWCs), respectively. Results by HTS revealed to phyla Proteobacteria (29–39%), Acidobacteria (17%), Actinobacteria (11–15%), and Bacteroidetes (5–12%) as the most abundant rhizobacterial taxa in rhizosphere samples. A total of 206 isolates (26 genera) were obtained with MWCs, where coincidentally with HTS, the most abundant phyla were Proteobacteria (70.4%), Firmicutes (24%), Actinobacteria (4%), and Bacteroidetes (1.5%). At the genus level, the most of isolates (72%) belonged to Pseudomonas, followed by Bacillus, Stenotrophomonas, Delftia, and Herbaspirillum. Members of rare taxa (Lelliottia, Rhodococcus, Micrococcus, Variovorax, and Bosea) also were isolated by MWCs. In addition, a high proportion (82%) of isolates showed high similarity with plant beneficial and environmental non-pathogenic bacteria whereas a minor proportion (18%) of isolates showed high similarity to human and plant pathogenic bacteria. This study demonstrates that in situ cultivation represents a useful tool to isolate a greater number of rhizobacterial taxa, which can be investigated under laboratory conditions in bioprospecting (e.g., plant growth–promoting bacteria) and public health (e.g., human opportunist and plant pathogens) studies.

Since the 1980s, plant growth‒promoting bacteria (PGPB) have been studied as a sustainable alternative to the use of chemical fertilizers to increase crop yields, and effective PGPB have been isolated from diverse plant (e.g., endosphere and phyllosphere) and soil (e.g., rhizosphere) compartments. Despite the promising plant growth promotion results commonly observed under laboratory and greenhouse conditions, the successful application of PGPB under field conditions has been limited, partly by the lack of knowledge of the ecological/environmental factors affecting the colonization, prevalence and activity of beneficial bacteria on crops. It is generally accepted that the effectiveness of PGPB depends on their ability to colonize a niche and compete with the indigenous plant microbiome under agronomic conditions. However, most studies do not include tracking or monitoring of PGPB in the environment after their application, and the beneficial effects on plants are measured by determining biomass‒ and physiology‒related parameters without confirming bacterial colonization. To date, methods based on reporter genes, immunological reactions and nucleic acids have been applied to track or monitor PGPB in seeds, soils or in planta after inoculation. In this review, we describe, compare and discuss the methods used for tracking and monitoring PGPB, including challenges and perspectives on some novel methods.

Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.

Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a &amp, Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.

1-Aminociclopropane-1-carboxylate (ACC)-degrading bacteria having been widely studied for their use in alleviating abiotic stresses in plants. In the present study, we isolated and characterized ACC-degrading bacteria from the rhizosphere, phyllosphere, and endosphere of the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis. One hundred and eighty of the 578 isolates (31%) were able to grow on minimal medium containing ACC, with 101 isolates (23, 37, and 41 endosphere-, phyllosphere- and rhizosphere-associated isolates, respectively) identified as being genetically unique by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Subsequently, freeze/thaw treatments and ice-recrystallization-inhibition (IRI) activity assays were performed, the results of which revealed that 77 (13%) of cold-tolerant isolates exhibited putative ACC deaminase activity. Significant (p &le, 0.05) differences in IRI activity were also observed between the studied plant niches. Surprisingly, all the cold-tolerant isolates showed ACC deaminase activity, independent of the plant niches, with 12 isolates showing the highest ACC deaminase activities of 13.21&ndash, 39.56 mmol &alpha, KB mg protein&minus, 1 h&minus, 1. These isolates were categorized as &lsquo, cold-tolerant hyper-ACC-degrading bacteria&rsquo, and identified as members of Pseudomonas, Serratia, and Staphylococcus genera. The results revealed the occurrence of cold-tolerant hyper-ACC-degrading bacteria in diverse plant niches of Antarctic vascular plants, that could be investigated as novel microbial inoculants to alleviate abiotic stresses in plants.

Flowering desert (FD) events consist of the rapid flowering of a wide variety of native plants in the Atacama Desert of Chile, which is categorized as the driest desert in the world. While ephemeral plants are an integral part of the desert ecosystem, there is little knowledge on plant-microbe interactions that occur during FD events. Consequently, the overall goals of this present study were to investigate changes in the composition and potential functions of rhizobacterial community of Cistanthe longiscapa (Montiaceae) during the 2014 and 2015 FD events and determine the composition, potential functions, and co-occurrence networks of rhizobacterial community associated with the root zone of C. longiscapa during pre- (PF) and full-flowering (FF) phenological stages. Results of this study showed that the Proteobacteria and Actinobacteria were the dominant taxa in rhizosphere soils during the three FD events (2014, 2015, and 2017) examined. In general, greater microbial richness and diversity were observed in rhizosphere soils during the 2015-, compared with the 2014-FD event. Similarly, predicted functional analyses indicated that a larger number of sequences were assigned to information processing (e.g., ion channel, transporters and ribosome) and metabolism (e.g., lipids, nitrogen, and sulfur) during 2015 compared with 2014. Despite the lack of significant differences in diversity among PF and FF stages, the combined analysis of rhizobacterial community data, along with data concerning rhizosphere soil properties, evidenced differences among both phenological stages and suggested that sodium is a relevant abiotic factor shaping the rhizosphere. In general, no significant differences in predicted functions (most of them assigned to chemoheterotrophy, magnesium metabolisms, and fermentation) were observed among PF and FF. Co-occurrence analysis revealed the complex rhizobacterial interactions that occur in C. longiscapa during FD, highlighting to Kouleothrixaceae family as keystone taxa. Taken together this study shows that the composition and function of rhizobacteria vary among and during FD events, where some bacterial groups and their activity may influence the growth and flowering of native plants, and therefore, the ecology and trophic webs in Atacama Desert.

Chile is among the largest avocado producers worldwide; however, currently, its production has diminished mainly attributed to abiotic stresses such as drought and soil salinity. Here, we evaluated the contribution of halotolerant bacterial consortia to water shortage and salt stress tolerance of avocado seedlings ( Persea americana Mill.) under field conditions. Inoculation trials were conducted in a commercial nursery to study the effects of two endophytic (C1 and C2) and two rhizosphere (C3 and C4) halotolerant bacterial consortia on growth, biomass, superoxide dismutase (SOD) and thiobarbituric acid reactive substances (TBARS) of avocado seedlings under salt (2% NaCl) stress and water shortage (50% less irrigation). Ours results revealed that avocado inoculation with C4 significantly ( P ≤ 0.05) increased aerial and root length; aerial and root fresh weight and chlorophyll content of salt-stressed seedlings; and the aerial length and root fresh weight of seedlings under water shortage. Similarly, the C4 significantly ( P ≤ 0.05) increased SOD activity in leaves of both the control and seedlings grown under salt stress and water shortage and also decreased TBARS content in leaves of control plants and of seedlings grown under salt stress. Whereas, C3 increased significantly ( P ≤ 0.05) aerial and root length and root fresh weight of salt-stressed seedlings; and also increased the trunk diameter and chlorophyll content of seedlings under water shortage. Similarly, C3 significantly ( P ≤ 0.05) stimulated SOD activity of leaves as compared to the control seedlings and also reduced the TBARS content of leaves and roots of avocado seedlings under salt stress. In contrast, the endophytic consortia were less efficient than rhizosphere consortia. Thus, C1 only increased the trunk diameter and chlorophyll content of salt–stressed seedlings and C2 increased the chlorophyll content of avocado seedlings under water shortage. Our study showed the favorable effect of bacterial inoculation on avocado nursey in nursery conditions under water shortage and salt stress, and identified consortia that potentially could be used as avocado biofertilizers.

Use of compost is a common agricultural practice. It improves soil fertility by adding nutrients and plant growth promoting (PGP) microorganisms. The role of bacterial-fungal interactions for compost-driven fertilization, however, is still poorly understood. In this study, we investigated whether putative PGP bacteria associate to and disperse along mycelia of fungal isolates. A ‘Fungal highway column system’ was used to isolate and characterize fungal—bacterial couples derived from commercial compost (C), non-composted bulk soil (BS) and rhizosphere soil with compost application (RSC). Bacterial-fungal couples were identified by 16S and 18S rRNA gene sequencing and isolated bacteria were tested for representative PGP traits. Couples of fungi and associated migrator bacteria were isolated from C and RSC only. They included the fungal genera Aspergillus, Mucor, Ulocladium, Rhizopus and Syncephalastrum, and the bacterial genera Rhodococcus, Bacillus, Pseudomonas, Agrobacterium, Glutamicibacter and Microbacterium. Many of migrator bacteria in RSC and C showed PGP traits (e.g., tryptophane—induced auxin synthesis or phytate mineralizing activity) suggesting that fungi contained in C and RSC allow for dispersal of putative PGP bacteria. Next to being provider of nutrients, compost may therefore be source for PGP bacteria and fungal mycelia serving as networks for their efficient dispersal.

The effects of arbuscular mycorrhizal (AM) inoculation on prokaryote abundance within the maize rhizosphere and hyphosphere, and retention of nutrients were investigated. Maize plants were grown in pots with a membrane located at a soil depth of approximately 16 cm that allowed growth of fungal hyphae above and below the membrane, but did not allow growth of roots below the membrane. As expected, mycorrhizal inoculation significantly increased the contents of soil organic matter, Total Kjeldahl Nitrogen (primarily organic N), and Mehlich 1 phosphorus relative to the non-inoculated control. Copy numbers of 16S rRNA genes were significantly higher in the mycorrhizal compartments relative to non-mycorrhizal controls. Bacterial ammonia monooxygenase (AOB) genes, but not archaeal monooxygease genes (AOA), were significantly higher in planted treatments with and without addition of mycorrhizae, indicating that mycorrhizae stimulate prokaryotic growth and bacterial nitrification. The ecological relevance of increased NOx-N resulting from the growth of AOB in inoculated soils is not clear; however, increased mobility of NOx-N over NH4 + could result in a competition between leaching loss and increased uptake by mycorrhizae.

Rhizobacterial communities may play a crucial role in phosphorus (P) nutrition of plants. However, our knowledge of how P fertilization modulates rhizobacterial communities in crops and pastures is still poor. Here, we investigated the effect of P addition (phosphate [PHO] and phytate [PHY]) on the composition of total bacterial communities and alkaline phosphomonoesterases (APase)-harboring bacterial populations in the rhizosphere microsites (root tip [RT] and mature zone [MZ]) of L. perenne. Sizes and diversities of bacterial communities were studied by 454-pyrosequencing of 16S rRNA genes, denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Our results suggested that phosphorus addition induces significant changes in the rhizobacterial community composition. Despite that pyrosequence analysis showed that members of the Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in all sampled rhizosphere microsites, differences in the relative abundances of some bacterial genera were detected (e.g., Arthrobacter and Acidothermus). Greater richness in rhizosphere microsites of plants supplied with PHY compared with PHO were revealed. With respect to APase-harboring bacterial populations, DGGE (phoD gene) showed significant differences between microsites supplied with PHO, PHY and controls. qPCR (16S rRNA genes, phoD and phoX) showed significantly greater abundances of bacteria and APase genes in RT than in MZ microsites. This study contributes to our understanding of the effect P fertilization on rhizobacterial community compositions of pastures grown in Chilean Andisols.

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.

Bacterial alkaline phosphomonoesterases (APases) are relevant for organic phosphorus (Po) recycling in many soils. However, the abundance and diversity of bacterial APase in the rhizospheres of native plants are poorly known, particularly in extreme environments. In this research work, we studied the composition of total and APase-harboring bacterial communities, abundances of selected APase genes (phoD and phoX), and APase activities in rhizosphere soils from native plants grown in extreme environments of northern (Atacama Desert), central (Andes volcano; Quetrupillan and Mamuil Malal) and hot spring (Liquine), and southern polar (Patagonia and Antarctic) regions of Chile. Differences in the composition of bacterial communities in the rhizosphere soils were revealed by denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) of 16S ribosomal RNA (rRNA), phoD, and phoX genes. In general, the significant lowest bacterial diversities, APase gene abundances, and APase activities were observed in rhizosphere soils from Atacama Desert, whereas the highest values were observed in rhizosphere soils of Patagonia. In addition, APase gene abundances were positively correlated among them and with APase activity of rhizosphere soils, but negatively correlated with phosphorus (P) availability in rhizosphere soils. Although bacterial APases were observed in all studied rhizosphere soils, their relevance to soil Po recycling in soils of extreme environments remains unclear and further studies are needed.

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(-1) year(-1)) without P significantly changed the composition of rhizobacterial communities. However, no significant community changes were observed with P (240 kg P ha(-1) year(-1)) and N-P application (270 kg N ha(-1) year(-1) plus 240 kg P ha(-1) year(-1)). In Site 2 (fertilized for 6 years with P; 400 kg P ha(-1) year(-1)), 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(-1) year(-1)). 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.

Cereal crops grown in southern Chilean Andisol provide suboptimal levels of this metalloid for human diet. Certain rhizosphere microorganisms, such as rhizobacteria and arbuscular mycorrhizal fungi can increase the selenium uptake in plants. The purpose of this study was to evaluate selenium acquisition by wheat plants through the co-inoculation of native selenobacteria strains (Stenotrophomonas sp. B19, Enterobacter sp. B16, Bacillus sp. R12 and Pseudomonas sp. R8), both individually and in mixture, as selenonanosphere source with one arbuscular mycorrhizal fungus (Glomus claroideum). Total selenium content in plant tissues and substrate was analyzed. According to our results, significant higher selenium content was found in inoculated plants in comparison to uninoculated controls (P ≤ 0.05). Independently of fungal presence, selenium content in grain from plants inoculated with Enterobacter sp. B16 (236 mg kg−1) was higher than the rest of the strains (116–164 mg kg−1). However, when plants were co-inoculated with a mixture of selenobacteria strains and G. claroideum, selenium content in grain was 23.5% higher (725 mg kg−1) than non-mycorrhizal plants (587 mg kg−1). The results suggest a synergistic effect between the selenobacteria mixture and G. claroideum associated to major biodiversity and demonstrate a great potential of these rhizosphere microorganisms for biofortification of cereals and its derivates., This study was supported by CONICYT Postdoctoral scholarship 3130542 and FONDECYT 1100625 of the Chilean Government. J.J. Acuña is thankful for the financial support of CONICYT through the Doctoral Fellowship Program. M.A. Jorquera also acknowledges financial support by FONDECYT 1120505.

Phytase-producing bacteria (PPB) is being investigated as plant growth promoting rhizobacteria (PGPR) to improve the phosphorus (P) nutrition and growth of plants grown in soil with high phytate content. Phytate is dominant organic P forms in many soils and must be hydrolyzed to be available for plants. Indian mustard (Brassica juncea) is a plant with economic importance in agriculture and phytoremediation, therefore biotechnological tools to improve growth and environmental stress tolerance are needed. In this study, we isolated and characterized PPB from Himalayan soils and evaluated their effect on growth and P uptake by B. juncea under greenhouse conditions. Sixty five PPB were isolated and based on phytate hydrolysis, three efficient PPB were chosen and identified as Acromobacter sp. PB-01, Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13. Selected PPB showed ability to grow at wide range of pH, temperature and salt concentrations as well as to harbour diverse PGPR activities, such as: solubilization of insoluble Ca-phosphate (193-642 μg ml(-1)), production of phytohormone indole acetic acid (5-39 μg ml(-1)) and siderophore. Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 showed 50 and 70 % inhibition of phytopathogen Rhizoctonia solani, respectively. Greenhouse potting assay also showed that the bacterization of B. juncea seeds with Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 significantly increased the biomass and P content in 30 days old seedlings. This study reveals the potential of PPB as PGPR to improve the growth of B. juncea.

In Chilean volcanic soil, crop production often is limited by a combination of the low available P and high concentration of toxic aluminum (Al). In this study we aimed to isolate Al-tolerant plant-growth-promoting bacteria from the rhizosphere and the endosphere of ryegrass grown in acidic Chilean volcanic soil in order to characterize a bacterial consortium capable of contributing to alleviation of Al 3+ toxicity and supporting plant growth in Andisol. Five strains, i.e. Klebsiella sp. RC3, Stenotrophomonas sp. RC5, Klebsiell a sp. RCJ4, Serratia sp. RCJ6 and Enterobacter sp. RJAL6, were selected based on their capacity to tolerate high Al concentration (10 mM) and to exhibit multiple plant-growth-promoting traits (P solubilization, indole acetic acid production, 1-aminocyclopropane-1-carboxylate deaminase activity, and exudation of organic acid anions and siderophores). Based on the results, we can suggest that selected bacteria could alleviate Al stress by forming Al 3+ -siderophore complexes. The plant-growth-promoting potential of the bacterial consortium was confirmed in an assay with ryegrass plants. In the treatment with cattle dung manure, the consortium promoted plant growth and the phosphatase activity in the rhizosphere soil. Increased phosphatase activity coincided with elevated P concentration in shoots. Our results suggest that a combination of native Al-tolerant bacteria and cattle dung manure is effective in decreasing Al toxicity and promoting plant growth in Andisols of southern Chile.

Plant growth-promoting rhizobacteria (PGPR) are studied as complements/alternatives to chemical fertilizers used in agriculture. However, poor information exists on the potential of PGPR from undisturbed ecosystems. Here, we have evaluated the plant growth-promoting (PGP) effect of rhizobacterial consortia from undisturbed Chilean arid ecosystems (Consortium C1) and agro-ecosystems (Consortium C2) on plant biomass production. The PGP effects of C1 and C2 were assayed in wheat seedlings (Triticum aestivum L.) grown in pots under growth chamber conditions and in pots placed in an open greenhouse under natural conditions, using two different Chilean Andisols (Piedras Negras and Freire series) kept either at 30 or 60% of their maximum water holding capacity (MWHC). PGP effects depended on the soil type, MWHC and the growth conditions tested. Although both consortia showed PGB effects in artificial soils relative to controls in growth chambers, only C1 provoked a PGP effect at 60% MWHC in phosphorus-poor soil of the 'Piedras Negras' series. At natural conditions, however, only C1 exhibited statistically significant PGP effects at 30% MWHC in 'Piedras Negras', yet and most importantly allowed to maintain similar plant biomass as at 60% MWHC. Our results support possible applications of rhizobacterial consortia from arid ecosystems to improve wheat growth in Chilean Andisols under water shortage conditions.Wheat seedling inoculated with rhizobacterial consortia obtained from an undisturbed Chilean arid ecosystem showed improved growth in phosphorus-poor and partly dry soil. Arid ecosystems should be considered in further studies as an alternative source of microbial inoculants for agro-ecosystems subjected to stressful conditions by low nutrients and/or adverse climate events.

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.

Cereal production in southern Chile is based on volcanic soils (Andisol) that are phosphorus (P) deficient for plant nutrition. Phytate-mineralizing rhizobacteria (PMR) have been suggested as soil inoculants to improve P uptake and growth of plants cultivated in P-deficient soils. In this study, a greenhouse experiment was conducted to investigate the effects of inoculation with PMR ( Bacillus sp. N1-19NA, Enterobacter sp. N0-29PA, Pseudomonas sp.N1-55PA and Serratia sp. N0-10LB) on biomass and P uptake of cereal plants (wheat, oat and barley) grown in a Chilean Andisol with out P fertilization. Results showed that inoculation with Enterobacter sp. N0-29PA significantly ( P ≤0.05) increased the biomass and Puptake of oat plants. Changes in rhizosphere properties as soil enzyme activities (acid phosphatase and urease), and auxin production potential were also produced by Enterobacter sp. N0-29PA inoculation. Despite the possible value, Enterobacter sp. N0-29PA as a soil inoculant for P-deficient soils, other PMR assayed did not consistently enhanced biomass and P uptake of plants. In addtion, polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) combined with non-metric multidimensional scaling (nMDS) analysis revealed that PMR inoculation induced changes in rhizobacterial community composition, suggesting that PMR application substantially modify the microbiological characteristics of rhizosphere. However, long-term studies at field level are still needed to practical use of PMR as inoculants in Chilean Andisols.

Management of soils to facilitate plant beneficial microbial interactions requires basic knowledge of the species composition and microbial community structures in the plant rhizosphere. Here, we examined composition of bacterial communities associated with rhizosphere microsites located at the root tips and mature root zones of Lolium perenne when grown in Chilean ash-derived volcanic soils (Andisols: Freire and Piedras Negras soil series). Community structures were analyzed by pyrosequencing of 16S ribosomal RNA (rRNA) genes followed by in silico analysis for phylogenetic assignments (MOTHUR and Visualization tool for Taxonomic Compositions of Microbial Community (VITCOMIC)). Analysis of the community structure revealed significant differences in community structures in relation to the soil series, which differed particularly in the relative abundance of Cyanobacteria and Firmicutes. However, no significant differences were observed with respect to root microsite location in the same Andisol series. Predominant taxa included members of the Proteobacteria, Actinobacteria, and Acidobacteria. Analysis by VITCOMIC showed that dominant bacterial groups comprised only 5 to 10 % of the total bacterial community and the remaining majority of bacteria included low-abundant taxa (Fusobacteria, Thermotogae, Lentisphaerae, Tenericutes, Deferribacteres Spirochaetes, Planctomycetes, Thermotogae, and Deinococcus-Thermus), most of which have not been previously reported or associated with the plant rhizosphere according to GenBank database. The results indicate that most of bacteria in the Chilean Andisols have not been described to the rhizosphere plants and their functional traits are still largely unknown.

Phytate-mineralizing rhizobacteria (PMR) perform an essential function for the mineralization of organic phosphorus but little is known about their ecology in soils and rhizosphere. In this study, PCR-based methods were developed for detection and quantification of the Bacillus β-propeller phytase (BPP) gene. Experiments were conducted to monitor the presence and persistence of a phytate-mineralizing strain, Bacillus sp. MQH19, after inoculation of soil microcosms and within the rhizosphere. The occurrence of the BPP gene in natural pasture soils from Chilean Andisols was also examined. The results showed that the Bacillus BPP gene was readily detected in sterile and nonsterile microcosms, and that the quantitative PCR (qPCR) methods could be used to monitor changes in the abundance of the BPP gene over time. Our results also show that the addition of phytate to nonsterile soils induced the expression of the BPP gene in the rhizosphere of ryegrass and the BPP gene was detected in all pasture soils sampled. This study shows that phytate addition soils induced changes in the abundance and expression of Bacillus BPP to genes in the rhizosphere and demonstrates that Bacillus BPP gene is cosmopolitan in pasture soils from Chilean Andisols.

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.

Plant growth-promoting rhizobacteria (PGPR) are common components of the rhizosphere, but their role in adaptation of plants to extreme environments is not yet understood. Here, we examined rhizobacteria associated with ancient clones of Larrea tridentata in the Mohave desert, including the 11,700-year-old King Clone, which is oldest known specimen of this species. Analysis of unculturable and culturable bacterial community by PCR-DGGE revealed taxa that have previously been described on agricultural plants. These taxa included species of Proteobacteria, Bacteroidetes, and Firmicutes that commonly carry traits associated with plant growth promotion, including genes encoding aminocyclopropane carboxylate deaminase and β-propeller phytase. The PGPR activities of three representative isolates from L. tridentata were further confirmed using cucumber plants to screen for plant growth promotion. This study provides an intriguing first view of the mutualistic bacteria that are associated with some of the world's oldest living plants and suggests that PGPR likely contribute to the adaptation of L. tridentata and other plant species to harsh environmental conditions in desert habitats.

Models of root colonization by bacteria facilitate conceptual and practical understanding of fundamental processes that influence plant health, mineral nutrition, and stress tolerance. In this study, we explored the use of cellular automata and agent-based models to simulate the primary colonization of roots by bacteria as determined by selected parameters related to bacterial growth (nutrient uptake, fitness, reproduction and starvation) and environmental constraints (space, nutrient depletion, and pH). The results were then compared with observations from experiments examining the colonization of plant roots by a GFP – strain of Escherichia coli . The latter experiments were conducted with plants grown in agar medium containing calcium phosphate that allowed visualization of bacterial distribution (aggregates and abundance) and phosphate solubilization at root microsites. The numerical models revealed outcomes for diverse numerical scenarios, which agreed with the in vivo data and provided a basic framework for describing bacterial colonization of plant roots. Further efforts will be required to evaluate factors affecting the competence and ecology of bacterial communities at rhizosphere microsites, but offer promise for the development of precise predictive models with practical applications for agriculture.

Plant growth-promoting rhizobacteria (PGPR) naturally occur in the rhizospheres of pasture, but still little is understood regarding how soil agricultural practices affect them. Here, we examined the effects of long-term nitrogen (N) fertilisation on the occurrence of potential culturable PGPR in rhizosphere soils from pastures grown in Chilean Andisols. We also evaluated in vitro the effects of organic acids (citric, malic and oxalic acids), metals (Al and Mn) and N supply (urea and ammonium sulphate) on indole acetic acid (IAA) production and phosphorus (P) liberation by selected strains. Compared with non-N-fertilised pasture, N fertilisation significantly increased (30%) the occurrence of culturable phosphobacteria but decreased (7%) the occurrence of IAA-producing rhizobacteria. Most efficient IAA-producing phosphobacteria were identified as Bacillus, Enterobacter, Pseudomonas and Serratia. At low pH (4.8), the assays showed that the IAA production by Serratia sp. N0-10LB was increased (31–74%) by organic acids. On the other hand, the IAA production by Pseudomonas sp. N1-55PA was increased two- to fivefold by metals. In all strains, the growth and IAA production were significant decreased by 500 μM of Al, except Serratia sp. N0-10LB, suggesting its potential as PGPR for Chilean Andisols. When urea was added as main N source, the bacterial growth and P utilisation significantly increased compared with ammonium sulphate. The influence of environmental factors that are typical of Chilean Andisols on rhizobacterial communities will provide better management practices to enhance their PGPR functions as well as a better selection biofertilisers to be used in Chilean Andisols.

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.

Rhizobacteria are capable of stimulating plant growth through a variety of mechanisms that include improvement of plant nutrition, production and regulation of phytohormones, and suppression of disease causing organisms. While considerable research has demonstrated their potential utility, the successful application of plant growth promoting rhizobacteria (PGPR) in the field has been limited by a lack of knowledge of ecological factors that determine their survival and activity in the plant rhizosphere. To be effective, PGPR must maintain a critical population density of active cells. Inoculation with PGPR strains can temporarily enhance the population size, but inoculants often have poor survival and compete with indigenous bacteria for available growth substrates. PGPR often have more than one mechanism for enhancing plant growth and experimental evidence suggests that the plant growth stimulation is the net result of multiple mechanisms of action that may be activated simultaneously. The aim of this review is to describe PGPR modes of action and discuss practical considerations for PGPR use in agriculture.

The rhizosphere is considered as a hot-spot for gene exchange among bacteria in terrestrial ecosystems. Chilean volcanic soils are characterized by low pH and high concentrations of aluminium (Al) in the soil solution, thus Al tolerance could be important for the survival of microorganisms in these soils; loss of genes encoding for Al tolerance may affect competitiveness particularly in the rhizosphere where competition is strong. The occurrence of Al-tolerance plasmids was investigated in the rhizospheres of pasture and crop plants growing in acidic volcanic soils from southern Chile. Al tolerance plasmids were captured by biparental mating. Two types of Al tolerance plasmids could be distinguished, based on their endonuclease restriction pattern. One plasmid of each group (denoted as pRPA21 and pOPA21) was selected for further studies. The plasmids showed a high stability in presence and absence of Al. Additionally, microbial community composition in the rhizosphere soils was assessed by denaturing gradient gel electrophoresis (DGGE). Sequencing of DGGE bands revealed among others, members of the bacterial phylum Gemmatimonadetes and archaeal phylum Crenarchaeota. The present study shows that the rhizosphere of pasture and crop plants growing in Chilean volcanic soil harbors genetic mobile elements which could play a role in the adaptation of bacterial populations to environmental stressors, such as Al-toxicity.

Chilean volcanic soils contain large amounts of total and organic phosphorus, but P availability is low. Phosphobacteria [phytate-mineralizing bacteria (PMB) and phosphate-solubilizing bacteria (PSB)] were isolated from the rhizosphere of perennial ryegrass (Lolium perenne), white clover (Trifolium repens), wheat (Triticum aestivum), oat (Avena sativa), and yellow lupin (Lupinus luteus) growing in volcanic soil. Six phosphobacteria were selected, based on their capacity to utilize both Na-phytate and Ca-phosphate on agar media (denoted as PMPSB), and characterized. The capacity of selected PMPSB to release inorganic P (Pi) from Na-phytate in broth was also assayed. The results showed that from 300 colonies randomly chosen on Luria–Bertani agar, phosphobacteria represented from 44% to 54% in perennial ryegrass, white clover, oat, and wheat rhizospheres. In contrast, phosphobacteria represented only 17% of colonies chosen from yellow lupin rhizosphere. This study also revealed that pasture plants (perennial ryegrass and white clover) have predominantly PMB in their rhizosphere, whereas PSB dominated in the rhizosphere of crops (oat and wheat). Selected PMPSB were genetically characterized as Pseudomonas, Enterobacter, and Pantoea; all showed the production of phosphoric hydrolases (alkaline phosphatase, acid phosphatase, and naphthol phosphohydrolase). Assays with PMPSB resulted in a higher Pi liberation compared with uninoculated controls and revealed also that the addition of glucose influenced the Pi-liberation capacity of some of the PMPSB assayed.