Genetic diversity of endophytic bacteria which could be find in the apoplastic sap of the medullary parenchym of the stem of healthy sugarcane plants

Development, Shelf Stability, and In-Vitro Evaluation of Liquid Bacterial Inoculant Acinetobacter lwoffii Strain PAU_31LN

Acinetobacter has been recognized as a versatile plant growth promoting (PGP) rhizobacteria (PGPR) that produce multiple PGP traits. The present study was conducted to formulate an efficient and stable liquid bacterial inoculant (LBI) of Acinetobacter lwoffii strain PAU_31LN. In the current investigation, total 16 endophytic bacteria were isolated from cotton leaves and evaluated for plant growth-promoting features such as production of phytohormones, mineral solubilization, siderophore production, hydrogen cyanide (HCN) production, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. The leaf endophytic bacteria designated as 31LN was found promising for all the PGP traits and it was identified as A. lwoffii strain PAU_31LN by 16S rRNA gene sequencing. For the development of LBI of A. lwoffii strain PAU_31LN, 4.5 g/L yeast extract, 5 g/L NaCl, 5 g/L peptone, and 12.5 mM food-grade trehalose was optimized as appropriate medium composition using response surface methodology (RSM) and Box-Behnken design. Further, the viability of A. lwoffii strain PAU_31LN in the optimized formulation was observed as 1.1 folds higher over the control after 180 days of storage at room temperature. Moreover, nonsignificant variation was recorded in the functional traits of 180 days old LBI of A. lwoffii strain PAU_31LN and freshly prepared LBI. The in-vitro plant growth parameters such as length and seed vigor index of 7-day-old cotton seedlings were enhanced by the seed bio-priming with LBI of A. lwoffii strain PAU_31LN over the control. The results of the present study signify the importance of endophytes and statistical methods to formulate prominent LBI.

Isolation of endophytic bacteria from the medicinal, forestal and ornamental tree Handroanthus impetiginosus

Plant interactions with endophytic bacteria produce mutual benefits and contribute to environmental sustainability. Handroanthus impetiginosus (Mart. ex DC.) Mattos 'pink lapacho' (syn. Tabebuia impetiginosa, Bignoniaceae) is a medicinal, ornamental and forestal native tree from South and Mesoamerica. Plant growth promoting bacteria (PGPB) isolated from pink lapacho are scarcely described. The aim of this work was to isolate and characterize native endophytic bacteria from pink lapacho. Ten bacterial strains were isolated from leaves and six from roots of naturally growing trees in Luján (Central-Eastern region of Argentina). Endophytes were identified as Bacillus, Paenibacillus, Pseudomonas, Rhizobium, Rummeliibacillus and Methylobacterium genera, according to 16S rRNA gene sequencing and phylogenetic analysis. In the present study, a strain of the Rummelibacillus genus (L14) has been first ever reported as endophyte. This strain was capable of growing in Nfb medium and exhibited zinc solubilization ability. A high percentage of strains showed PGPB traits; namely 88% fixed nitrogen, 63% solubilized zinc, 69% solubilized phosphate and 63% produced indole compounds such as IAA. Most strains were salt tolerant that confer them a potential competitive advantage to survive in saline conditions. To the best of our knowledge, this is the first study reporting an approach to assess the diversity of cultivable endophytic bacteria of H. impetiginosus tree and its plant growth promoting capacity. The knowledge about this kind of associations could contribute to environmental sustainability by developing effective biofertilizers that minimize the use of chemical fertilizers and pesticides.

Endophytic microflora from Ficus carica L. leaves – isolation, characterization and potential for application

Fig leaves (Ficus carica L.) are widely used in traditional medicine as a remedy or for prevention of many health problems (lowering blood sugar and triglyceride levels, cardiovascular diseases, etc.). The aim of the research was isolation of endophytic microflora, its characterization and proving its potential for future application. Two endophytic bacteria Streptococcus sp. Fcl1 and Kocuria rhizophila Fcl20 were isolated from the fig leaves and characterized. Using HPLC method was also determined the polyphenolic profile of aqueous-alcoholic extract (70% (v/v) ethanol) and microwave-assisted aqueous extract of fig leaves, for the purpose of phytochemical characterization of the plant, for subsequent study of the endophyte-plant relationship. The main found phenolic acids and flavonoids in extracts were: (+)-catechin, vanillic acid, syringic acid, (-)-epicatechin, ferulic acid, salicylic acid, rosmarinic acid, rutin.

The Effect of Inoculation of a Diazotrophic Bacterial Consortium on the Indigenous Bacterial Community Structure of Sugarcane Apoplast Fluid

The extracellular space in plants, termed the apoplast, has a pH and sugar content that enables bacterial growth and represents a possible niche for the establishment of endophytic bacteria. Previous studies have investigated the effects of diazotrophic bacteria inoculation in sugarcane varieties, but it has not yet been analyzed how the microbial community of apoplast fluid of sugarcane is affected. High-throughput next generation sequencing of the 16S rRNA gene was used throughout this study to determine the effect of inoculation with a diazotrophic bacteria consortium, previously isolated from sugarcane, on the native bacterial population of sugarcane variety RB867515 grown in the field. The analyses were carried out 450 days after inoculation. The results revealed the presence of 22 phyla, with predominance of Proteobacteria phylum. It was observed that the inoculated consortium changed the indigenous bacterial community structure of sugarcane apoplast fluid by decreasing diversity and evenness, interfering in the composition of rare species. Microbial community composition analysis revealed differences between treatments. The differential abundance test showed there were 43 amplicon sequence variants (ASVs) which were relatively more abundant in the inoculated treatment, with predominance of the Sphingomonas genus. The predicted functions of the most abundant ASVs revealed the presence of genera related to plant growth promotion and protection against phytopathogens. Analysis to evaluate the occurrence of inoculated strains in the recovered data was not conclusive since the ASVs taxonomically close to the inoculated bacteria were observed in low abundance. The present study is the first report to elucidate the bacterial community in sugarcane apoplast fluid using a culture-independent approach. It demonstrated that the diazotrophic bacterial consortium interferes in the natural bacterial community in sugarcane variety RB867515.

Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control

Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders. In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer, our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen, since there is no efficient chemical or biological control method for this pest. Therefore, endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid, central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil. The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus. The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%). BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract, while the B. cereus group remained very closely clustered in the dendrogram. According to XRE biomarker analysis, eleven strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) correspond to B. thuringiensis species. Additional studies using conserved genes (glp, gmk, pta, and tpi) indicated that most of these strains were phylogenetically closely related to B. thuringiensis and may be considered different subspecies. In conclusion, this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time. These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B. thuringiensis species.

Alternative Hosts in the Families Poaceae and Cyperaceae for Xanthomonas vasicola pv. vasculorum, Causal Agent of Bacterial Leaf Streak of Corn

The bacterial pathogen Xanthomonas vasicola pv. vasculorum was first reported in the United States causing bacterial leaf streak on Nebraska corn (Zea mays) in 2016. The bacterium is also known to cause disease in sugarcane, grain sorghum, broom bamboo, and various palm species. The objective of this study was to identify alternative hosts for X. vasicola pv. vasculorum among plants commonly found in corn growing areas of the United States. In repeated greenhouse experiments, 53 species of plants found in the United States that had not been tested previously for susceptibility to X. vasicola pv. vasculorum were inoculated with the pathogen and monitored for symptom development. Eleven species in the family Poaceae exhibited symptoms: oat (Avena sativa), rice (Oryza sativa), orchardgrass (Dactylis glomerata), indiangrass (Sorghastrum nutans), big bluestem (Andropogon gerardii), little bluestem (Schizachyrium scoparium), timothy (Phleum pratense), sand bluestem (Andropogon hallii), green foxtail (Setaria viridis), bristly foxtail (Setaria verticillata), and johnsongrass (Sorghum halepense). Yellow nutsedge (Cyperus esculentus) in the Cyperaceae also was a symptomatic host. In addition, endophytic colonization by X. vasicola pv. vasculorum was found in three asymptomatic alternative hosts: downy brome (Bromus tectorum), tall fescue (Festuca arundinacea), and western wheatgrass (Pascopyum smithii). Experiments were also conducted in the field to determine the potential for alternative hosts to become infected by natural inoculum. Symptoms developed only in big bluestem and bristly foxtail in field experiments. These results suggest that infection of alternative hosts by X. vasicola pv. vasculorum can occur, but infection rates might be limited by environmental conditions.

Diversity of nitrogen-fixing rhizobacteria associated with sugarcane: a comprehensive study of plant-microbe interactions for growth enhancement in Saccharum spp

BACKGROUND

Nitrogen is an essential element for sugarcane growth and development and is generally applied in the form of urea often much more than at recommended rates, causing serious soil degradation, particularly soil acidification, as well as groundwater and air pollution. In spite of the importance of nitrogen for plant growth, fewer reports are available to understand the application and biological role of N2 fixing bacteria to improve N2 nutrition in the sugarcane plant.

RESULTS

In this study, a total of 350 different bacterial strains were isolated from rhizospheric soil samples of the sugarcane plants. Out of these, 22 isolates were selected based on plant growth promotion traits, biocontrol, and nitrogenase activity. The presence and activity of the nifH gene and the ability of nitrogen-fixation proved that all 22 selected strains have the ability to fix nitrogen. These strains were used to perform 16S rRNA and rpoB genes for their identification. The resulted amplicons were sequenced and phylogenetic analysis was constructed. Among the screened strains for nitrogen fixation, CY5 (Bacillus megaterium) and CA1 (Bacillus mycoides) were the most prominent. These two strains were examined for functional diversity using Biolog phenotyping, which confirmed the consumption of diverse carbon and nitrogen sources and tolerance to low pH and osmotic stress. The inoculated bacterial strains colonized the sugarcane rhizosphere successfully and were mostly located in root and leaf. The expression of the nifH gene in both sugarcane varieties (GT11 and GXB9) inoculated with CY5 and CA1 was confirmed. The gene expression studies showed enhanced expression of genes of various enzymes such as catalase, phenylalanine-ammonia-lyase, superoxide dismutase, chitinase and glucanase in bacterial-inoculated sugarcane plants.

CONCLUSION

The results showed that a substantial number of Bacillus isolates have N-fixation and biocontrol property against two sugarcane pathogens Sporisorium scitamineum and Ceratocystis paradoxa. The increased activity of genes controlling free radical metabolism may at least in part accounts for the increased tolerance to pathogens. Nitrogen-fixation was confirmed in sugarcane inoculated with B. megaterium and B. mycoides strains using N-balance and 15N2 isotope dilution in different plant parts of sugarcane. This is the first report of Bacillus mycoides as a nitrogen-fixing rhizobacterium in sugarcane.

Evolutionary insights into adaptation of Staphylococcus haemolyticus to human and non-human niches

Staphylococcus haemolyticus is a well-known member of human skin microbiome and an emerging opportunistic human pathogen. Presently, evolutionary studies are limited to human isolates even though it is reported from plants with beneficial properties and in environmental settings. In the present study, we report isolation of novel S. haemolyticus strains from surface sterilized rice seeds and compare their genome to other isolates from diverse niches available in public domain. The study showed expanding nature of pan-genome and revealed set of genes with putative functions related to its adaptability. This is seen by presence of type II lanthipeptide cluster in rice isolates, metal homeostasis genes in an isolate from copper coin and gene encoding methicillin resistance in human isolates. The present study on differential genome dynamics and role of horizontal gene transfers has provided novel insights into capability for ecological diversification of a bacterium of significance to human health.

Prospecting Plant Growth-Promoting Bacteria Isolated from the Rhizosphere of Sugarcane Under Drought Stress

In the rhizosphere, the soil bacteria and the plants are closely related, with the plant-associated microbiota playing an important role in promoting plant growth under both normal and stress conditions. In this study, the cultivable bacteria in the sugarcane rhizosphere under different levels of drought stress were characterized and screened for plant growth activities. The results suggested that the microbial community associated with the sugarcane rhizosphere was strongly affected by drought, but some important genera of bacteria such as Arthrobacter, Pseudomonas, Microbacterium, and Bacillus remained present during the entire experiment, indicating the adaptability of these organisms and their importance in the rhizosphere community. Many isolates exhibited positive results for one or more plant growth activity, and they were also capable of growing under simulated drought stress, suggesting that the microorganisms isolated from the sugarcane rhizosphere could be explored for uses such as biofertilizers or biocontrol agents in agriculture.

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

Endophytic bacteria are nearly ubiquitously present in the internal tissues of plants, and some endophytes can promote plant growth. In this study, we sampled the roots of four ancestral species of sugarcane (two genotypes per species) and two sugarcane cultivars, and used 16S rRNA and nifH gene sequencing to characterize the root endophytic bacterial communities and diazotroph diversity. A total of 7,198 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. The endophytic bacterial communities exhibited significantly different α- and β-diversities. From the 202 detected families in the sugarcane roots, a core microbiome containing 13 families was identified. The nifH gene was successfully detected in 9 of 30 samples from the four sugarcane species assayed, and 1,734 OTUs were merged for endophytic diazotrophs. In the tested samples, 43 families of endophytic diazotrophs were detected, and six families showed differences across samples. Among the 20 most abundant detected genera, 10 have been reported to be involved in nitrogen fixation in sugarcane. These findings demonstrate the diversity of the microbial communities in different sugarcane germplasms and shed light on the mechanism of biological nitrogen fixation in sugarcane.

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases

The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.

Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters

Endophytic actinobacteria, which reside in the inner tissues of host plants, are gaining serious attention due to their capacity to produce a plethora of secondary metabolites (e.g. antibiotics) possessing a wide variety of biological activity with diverse functions. This review encompasses the recent reports on endophytic actinobacterial species diversity, in planta habitats and mechanisms underlying their mode of entry into plants. Besides, their metabolic potential, novel bioactive compounds they produce and mechanisms to unravel their hidden metabolic repertoire by activation of cryptic or silent biosynthetic gene clusters (BGCs) for eliciting novel secondary metabolite production are discussed. The study also reviews the classical conservative techniques (chemical/biological/physical elicitation, co-culturing) as well as modern microbiology tools (e.g. next generation sequencing) that are being gainfully employed to uncover the vast hidden scaffolds for novel secondary metabolites produced by these endophytes, which would subsequently herald a revolution in drug engineering. The potential role of these endophytes in the agro-environment as promising biological candidates for inhibition of phytopathogens and the way forward to thoroughly exploit this unique microbial community by inducing expression of cryptic BGCs for encoding unseen products with novel therapeutic properties are also discussed.

Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth

The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd.

Influencia de diferentes factores en el crecimiento de bacterias endófitas de caña de azúcar

<p><strong>Título en ingles:</strong> <strong>Influence of different factors in the growth of endophytic bacteria of sugarcane</strong></p><p>En Cuba, entre los esfuerzos por lograr la sostenibilidad en la agricultura se han empleado biopreparados a gran escala, los cuales han tenido un gran impacto económico, ecológico y social. La caña de azúcar constituye uno de los principales cultivos agrícolas para nuestro país y tiene gran importancia desde los puntos de vista económico y ecológico a nivel mundial. En el presente trabajo se demostró el efecto de diferentes fuentes de carbono y nitrógeno en el crecimiento de 5 cepas endófitas de caña de azúcar, 3 de <em>Gluconacetobacter diazotrophicus</em>, una de <em>Bacillus licheniformis</em> y una de <em>Enterobacter agglomerans</em>. De igual forma, se estudió la influencia de jugos provenientes de cinco variedades, así como diferentes concentraciones de las fitohormonas ácido 3 indolacético (AIA) y ácido giberélico (GA) en el crecimiento. Se demostró que la asparagina y el sulfato de amonio como fuentes de nitrógeno adicionadas al medio LGI posibilitan un mayor crecimiento de las bacterias endófitas estudiadas. El medio LGI suplementado con jugo de caña de azúcar favorece significativamente (p≤0,05) el crecimiento de los microorganismos endófitos y no existe relación directa entre el origen varietal del jugo y de las cepas. Por otra parte las fitohormonas en bajas concentraciones favorecieron el crecimiento, no ocurriendo así cuando se encuentran a elevadas concentraciones en el medio de cultivo. Es necesario estudiar todos los factores que pueden influir en la interacción entre la planta y los endófitos para poder utilizar sus potencialidades como promotores del crecimiento vegetal.</p>

Signaling in the phytomicrobiome: breadth and potential

Higher plants have evolved intimate, complex, subtle, and relatively constant relationships with a suite of microbes, the phytomicrobiome. Over the last few decades we have learned that plants and microbes can use molecular signals to communicate. This is well-established for the legume-rhizobia nitrogen-fixing symbiosis, and reasonably elucidated for mycorrhizal associations. Bacteria within the phytomircobiome communicate among themselves through quorum sensing and other mechanisms. Plants also detect materials produced by potential pathogens and activate pathogen-response systems. This intercommunication dictates aspects of plant development, architecture, and productivity. Understanding this signaling via biochemical, genomics, proteomics, and metabolomic studies has added valuable knowledge regarding development of effective, low-cost, eco-friendly crop inputs that reduce fossil fuel intense inputs. This knowledge underpins phytomicrobiome engineering: manipulating the beneficial consortia that manufacture signals/products that improve the ability of the plant-phytomicrobiome community to deal with various soil and climatic conditions, leading to enhanced overall crop plant productivity.

Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6

Xylella fastidiosa, the causal agent of citrus variegated chlorosis (CVC), colonizes plant xylem, reducing sap flow, and inducing internerval chlorosis, leaf size reduction, necrosis, and harder and smaller fruits. This bacterium may be transmitted from plant to plant by sharpshooter insects, including Bucephalogonia xanthopis. The citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 colonizes citrus xylem and previous studies showed that this strain is also transferred from plant to plant by B. xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta and inside the insect vector during co-transmission by the same insect vector. To better understand the X. fastidiosa behavior in the presence of M. mesophilicum, we evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. The results showed that during co-cultivation, X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium.

Isolation of cellulolytic bacteria from the intestine of Diatraea saccharalis larvae and evaluation of their capacity to degrade sugarcane biomass

As a strategy to find efficient lignocellulose degrading enzymes/microorganisms for sugarcane biomass pretreatment purposes, 118 culturable bacterial strains were isolated from intestines of sugarcane-fed larvae of the moth Diatraea saccharalis. All strains were tested for cellulolytic activity using soluble carboxymethyl cellulose (CMC) degrading assays or by growing bacteria on sugarcane biomass as sole carbon sources. Out of the 118 strains isolated thirty eight were found to possess cellulose degrading activity and phylogenetic studies of the 16S rDNA sequence revealed that all cellulolytic strains belonged to the phyla γ-Proteobacteria, Actinobacteria and Firmicutes. Within the three phyla, species belonging to five different genera were identified (Klebsiella, Stenotrophomonas, Microbacterium, Bacillus and Enterococcus). Bacterial growth on sugarcane biomass as well as extracellular endo-glucanase activity induced on soluble cellulose was found to be highest in species belonging to genera Bacillus and Klebsiella. Good cellulolytic activity correlated with high extracellular protein concentrations. In addition, scanning microscopy studies revealed attachment of cellulolytic strains to different sugarcane substrates. The results of this study indicate the possibility to find efficient cellulose degrading enzymes and microorganisms from intestines of insect larvae feeding on sugarcane and their possible application in industrial processing of sugarcane biomass such as second generation biofuel production.

Changes in the population of seed bacteria of transgenerationally Cd-exposed Arabidopsis thaliana

Plant-associated bacteria can have beneficial effects on the growth and health of their host. Nevertheless, the role of endophytic bacteria present in seeds has not been investigated in depth. In this study, the cultivable endophytic population of seeds from Arabidopsis thaliana exposed to 2 μm cadmium for several generations (Cd seeds) was compared with a population isolated from seeds of plants that were never exposed to Cd (control seeds). We observed obvious differences between the two types of seed concerning genera present and phenotypic characteristics of the different isolates. Sinorhizobium sp. and Micrococcus sp. were only found in control seeds, while Pseudomonas sp., Bosea sp. and Paenibacillus sp. were only found in Cd seeds. Sphingomonas sp., Rhizobium sp., Acidovorax sp., Variovorax sp., Methylobacterium sp., Bacillus sp. and Staphylococcus sp. occurred in varying numbers in both types of seed. Metal tolerance and 1-aminocyclopropane-1-carboxylate deaminase activity were predominantly found in strains isolated from Cd seeds, while the production of siderophores, indole-3-acetic acid and organic acids was more prevalent in endophytes isolated from control seeds. These data support the hypothesis that certain endophytes are selected for transfer to the next generation and that their presence might be important for subsequent germination and early seedling development.

Endophytic microbial diversity in coffee cherries of Coffea arabica from southeastern Brazil

The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction - denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.

Microbes - friends and foes of sugarcane

Sugarcane is an important cash crop for many countries because it is a major source of several products including sugar and bioethanol. To obtain maximum yields there is a need to apply large quantities of chemical fertilizers.Worldwide yields are also severely affected by more than sixty diseases, mostly caused by fungi but viruses, phytoplasmas, nematodes and other pests can also damage this crop. For most of these diseases, chemical control is not available and breeders are struggling with the development of pest resistant varieties. Many members of the grass family Poaceae establish associations with beneficial microbes which promote their growth by direct and indirect mechanisms. They can be used as means to reduce the need for chemical fertilizer and to minimize the impacts of pathogen invasion. This review highlights the diversity of the microbes associated with sugarcane and the role of beneficial microbes for growth promotion and biocontrol. More extensive use of beneficial microbes will help the sugarcane grower not only to reduce the use of chemical fertilizers but also minimize the disease. In this paper, a brief description of both the non-pathogenic and pathogenic microbes associated with sugarcane is provided. Future prospects for the expanded use of beneficial microbes for sugarcane are also discussed and detailed herein.

Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods

Endophytes are now considered as an important component of biodiversity. However, the diversity of endophytic actinobacteria associated with tropical rainforest native medicinal plants is essentially unknown. In this study, the diversity of endophytic actinobacteria residing in root, stem and leaf tissues of medicinal plant Maytenus austroyunnanensis collected from tropical rainforest in Xishuangbanna, China was investigated with a combination of cultivation and culture-independent analysis on the basis of 16S rRNA gene sequencing. By using different selective isolation media and methods, a total of 312 actinobacteria were obtained, and they were affiliated with the order Actinomycetales (distributed into 21 genera). Based on a protocol for endophytes enrichment, three 16S rRNA gene clone libraries were constructed and 84 distinct operational taxonomic units were identified and they distributed among the orders Actinomycetales and Acidimicrobiales, including eight suborders and at least 38 genera with a number of rare actinobacteria genera. Phylogenetic analysis showed that 32% of the clones in the libraries had lower than 97% similarities with related type strains. Interestingly, six genera from the order Actinomycetales and uncultured clones from Acidimicrobiales have not, to our knowledge, been previously reported as endophytes. Our study confirms abundant endophytic actinobacterial consortium in tropical rainforest native plant and suggests that this special habitat represents an underexplored reservoir of diverse and novel actinobacteria of potential interest for bioactive compounds discovery.

Diversity and isolation of rare actinomycetes: an overview

A renewed interest in the development of new antimicrobial agents is urgently needed to combat the increasing number of antibiotic-resistant strains of pathogenic microorganisms. Actinomycetes continue to be the mainstream supplier of antibiotics used in industry. The likelihood of discovering a new compound with novel chemical structure can be increased with intensive efforts in isolating and screening of rare genera of microorganisms to include in natural-product-screening collections. An unexpected variety of rare actinomycetes is now being isolated worldwide from previously uninvestigated diverse natural habitats, using different selective isolation methods. These isolation efforts include methods to enhance growth (enrichment) of rare actinomycetes, and eliminate unwanted microorganisms (pretreatment). To speed up the strain isolation process, knowledge about the distribution of such unexploited groups of microorganisms must also be augmented. This is a summary of using these microorganisms as new potential biological resources, and a review of almost all of the selective isolation methods, including pretreatment and enrichment techniques that have been developed to date for the isolation of rare actinomycetes.

Diversity and community structure of culturable arsenic-resistant bacteria across a soil arsenic gradient at an abandoned tungsten-tin mining area

We studied the bacterial diversity at a single location (the Terrubias mine; Salamanca province, Spain) with a gradient of soil As contamination to test if increasing levels of As would (1) change the preponderant groups of arsenic-resistant bacteria and (2) increase the tolerance thresholds to arsenite [As(III)] and arsenate [As(V)] of such bacteria. We studied the genetic and taxonomic diversity of culturable arsenic-resistant bacteria by PCR fingerprinting techniques and 16S rRNA gene sequencing. Then, the tolerance thresholds to As(III) and As(V) were determined for representative strains and mathematically analyzed to determine relationships between tolerances to As(III) and As(V), as well as these tolerances with the soil contamination level. The diversity of the bacterial community was, as expected, inversely related to the soil As content. The overall preponderant arsenic-resistant bacteria were Firmicutes (mainly Bacillus spp.) followed by γ-Proteobacteria (mainly Pseudomonas spp.), with increasing relative frequencies of the former as the soil arsenic concentration increased. Moreover, a strain of the species Rahnella aquatilis (γ-Proteobacteria class) exhibited strong endurance to arsenic, being described for the first time in literature such a phenotype within this bacterial species. Tolerances of the isolates to As(III) and As(V) were correlated but not with their origin (soil contamination level). Most of the strains (64%) showed relatively low tolerances to As(III) and As(V), but the second most numerous group of isolates (19%) showed increased tolerance to As(III) rather than to As(V), even though the As(V) anion is the prevalent arsenic species in soil solution at this location. To our knowledge, this is the first study to report a shift towards preponderance of Gram-positive bacteria (Firmicutes) related to high concentrations of soil arsenic. It was also shown that, under aerobic conditions, strains with relatively enhanced tolerance to As(III) predominated over the most As(V)-tolerant ones.

Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity

The deterioration of the stone built and sculptural heritage has prompted the search and development of novel consolidation/protection treatments that can overcome the limitations of traditional ones. Attention has been drawn to bioconservation, particularly bacterial carbonatogenesis (i.e. bacterially induced calcium carbonate precipitation), as a new environmentally friendly effective conservation strategy, especially suitable for carbonate stones. Here, we study the effects of an in situ bacterial bioconsolidation treatment applied on porous limestone (calcarenite) in the sixteenth century San Jeronimo Monastery in Granada, Spain. The treatment consisted in the application of a nutritional solution (with and without Myxococcus xanthus inoculation) on decayed calcarenite stone blocks. The treatment promoted the development of heterotrophic bacteria able to induce carbonatogenesis. Both the consolidation effect of the treatment and the response of the culturable bacterial community present in the decayed stone were evaluated. A significant surface strengthening (consolidation) of the stone, without altering its surface appearance or inducing any detrimental side effect, was achieved upon application of the nutritional solution. The treatment efficacy was independent of the presence of M. xanthus (which is known as an effective carbonatogenic bacterium). The genetic diversity of 116 bacterial strains isolated from the stone, of which 113 strains showed carbonatogenic activity, was analysed by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) and 16S rRNA gene sequencing. The strains were distributed into 31 groups on the basis of their REP-PCR patterns, and a representative strain of each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that isolates belong to a wide variety of phylogenetic groups being closely related to species of 15 genera within the Proteobacteria, Firmicutes and the Actinobacteria. This study shows that the abundant carbonatogenic bacteria present in the decayed stone are able to effectively consolidate the degraded stone by producing new calcite (and vaterite) cement if an adequate nutritional solution is used. The implications of these results for the conservation of cultural heritage are discussed.

Acinetobacter strains IH9 and OCI1, two rhizospheric phosphate solubilizing isolates able to promote plant growth, constitute a new genomovar of Acinetobacter calcoaceticus

During a screening of phosphate solubilizing bacteria (PSB) in agricultural soils, two strains, IH9 and OCI1, were isolated from the rhizosphere of grasses in Spain, and they showed a high ability to solubilize phosphate in vitro. Inoculation experiments in chickpea and barley were conducted with both strains and the results demonstrated their ability to promote plant growth. The 16S rRNA gene sequences of these strains were nearly identical to each other and to those of Acinetobacter calcoaceticus DSM 30006(T), as well as the strain CIP 70.29 representing genomospecies 3. Their phenotypic characteristics also coincided with those of strains forming the A. calcoaceticus-baumannii complex. They differed from A. calcoaceticus in the utilization of l-tartrate as a carbon source and from genomospecies 3 in the use of d-asparagine as a carbon source. The 16S-23S intergenic spacer (ITS) sequences of the two isolates showed nearly 98% identities to those of A. calcoaceticus, confirming that they belong to this phylogenetic group. However, the isolates appeared as a separate branch from the A. calcoaceticus sequences, indicating their molecular separation from other A. calcoaceticus strains. The analysis of three housekeeping genes, recA, rpoD and gyrB, confirmed that IH9 and OCI1 form a distinct lineage within A. calcoaceticus. These results were congruent with those from DNA-DNA hybridization, indicating that strains IH9 and OCI1 constitute a new genomovar for which we propose the name A. calcoaceticus genomovar rhizosphaerae.