Plant Cell Tiss Organ Cult DOI 10.1007/s11240-016-1144-9

REVIEW

Bacteria in the plant tissue culture environment Teresa Orlikowska1 · Katarzyna Nowak1 · Barbara Reed2 

Received: 28 June 2016 / Accepted: 26 November 2016 © Springer Science+Business Media Dordrecht (outside the USA) 2016

Abstract Bacteria and plants are joined in various symbiotic relationships that have developed over millennia and have inluenced the evolution of both groups. Bacteria inhabit the surfaces of most plants and are also present inside many plant organs. These bacteria may have positive, neutral or negative impacts on their plant hosts. Probiotic efects may improve plant nutrition or increase resistance to biotic and abiotic stresses. Conversely pathogenic bacteria may kill or reduce the vigor of plant hosts. In addition some bacteria inhabit plants and proit from excess metabolites or shelter while not injuring the plant. Micropropagation of plants is based on the stimulation of organogenesis or embryogenesis from explants that are supericially decontaminated and placed into a sterile environment. If successful, this process removes bacteria from surfaces, but those inhabiting inner tissues and organs are usually not afected by these steriliants. In vitro conditions are designed for optimal plant growth and development, however these conditions are also often ideal for bacterial multiplication. The presence of bacteria in the in vitro environment was almost universally considered negative for plant culture, but more recently this view has been questioned. Certain bacteria appear to have a beneicial efect on the explants in culture; increasing multiplication and * Barbara Reed [email protected] Teresa Orlikowska [email protected] Katarzyna Nowak [email protected] 1

Research Institute of Horticulture, Skierniewice, Poland

2

Department of Horticulture, Oregon State University and U S Department of Agriculture, Corvallis, OR, USA

rooting, increasing explant quality, and organo- and embryogenesis of recalcitrant genotypes. The most important role of beneicial bacteria for micropropagated plants is likely to be during acclimatization, when growth is resumed under natural conditions. This review includes the role of bacterial interactions in plants, especially those grown in vitro. Keywords Beneicial bacteria · Biotization · Burkholderia · Contamination · Stress · Symbiosis

The role of bacteria in plants Plant-associated bacteria form both epiphytic and endophytic populations throughout plants (Compant et al. 2011; Friesen et  al. 2011; Turner et  al. 2013), including meristematic cells (detected using in-situ hybridization) (Pirttilä et al. 2000) or pollen (Madmony et al. 2005). Such colonizing populations of bacteria and other microorganisms are recognized as the host’s microbiome (Turner et  al. 2013) also referred to as its “second genome” (Berg et al. 2014). Thus plants in their natural environment, like any other eukaryote or prokaryote, are holobionts (Hardoim et  al. 2008; Rosenberg et  al. 2010), also known as superorganisms (Podolich et  al. 2009), meta-organisms (Berg et  al. 2014) or pan-genomes (Turner et  al. 2013), and may be considered as expanded phenotypes (Meldau et  al. 2012). This co-habitation may extend the life potential of the partners (Rout et al. 2013). Bacteria have accompanied higher organisms from their beginning, thus participating in their creation and evolution (Rosenberg et  al. 2010). Bacteria-host plant interactions are classiied as commensalistic, mutualistic or antagonistic (Senthilkumar et  al. 2008, 2011; Vacheron et  al. 2013). The most plant contact with bacteria

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takes place in the root zone, where a wide range of bacteria live, where bacterial and plant metabolites mediate the establishment of contacts, and where penetration into the roots occurs. Bacteria can also enter plants through leaves, lowers, stems and cotyledons. A frequent outcome is the colonization of the whole plant (Compant et  al. 2008a). Bacteria can be transmitted across plant generations, either vertically through generative organs, or horizontally via vegetative propagules (Partida-Martinez and Heil 2011). Plant endophytes are those organisms that live throughout the whole, or a part of the life cycle within living plant tissue, without causing symptoms of disease (Wilson 1995). Endophytes can afect physiological processes of the plant, to an extent not unlike the plant genotype (Sessitsch et  al. 2012), as a source of metabolites similar to, or different from, those produced by plants (Brader et al. 2014; Ludwig-Müller 2015a). Therefore, in any examination of individual functional characteristics of plants it is obligatory to take into account not only the traits resulting from the plant genotype, but also from the genotypes of endophytic microorganisms that inhabit it (Friesen et al. 2011). Some endophytes are known to be highly speciic to the host genotype, but others have a broader range of potential hosts (Hardoim et al. 2011). In nature, a microbiome is usually speciic to plants of the same species (Berg and Smalla 2009) growing in the same conditions. Nevertheless, it is shaped by internal and external factors, being much richer in the roots than in the above ground parts. Badri et al. (2013) argued that plants’ phenolic components and their derivatives secreted by the roots modify the composition of the rhizosphere microbiome, conirming the active role of plants in recruitment of bacteria (Turner et  al. 2013). However, according to Santhanam et al. (2015), a study carried out on Nicotiana attenuata revealed that the major driver of the variability in root bacterial communities is a local soil niche from which bacteria move into plant roots. When bacteria useful to plants are discovered, it would be important to determine whether they are speciically associated with a host genotype or whether they will also be able to colonize other genotypes and enter into similar interactions. Both of these variants are possible (Ma et al. 2011), due to strong bacterial versatility and speciicity in relation to plants, and because the plant response, that to some extent can control the level of bacterial colonization in qualitative and quantitative terms (Hardoim et al. 2008). Plants react defensively to pathogenic microorganisms but also encourage those beneicial to their own survival (Oldroyd 2013). Several mechanisms of recognition were discovered but the inal result depends on both, signals released by bacteria and plant receptors (Carvalho et  al. 2016).

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Beneits of plant-bacteria association Beneits can vary depending on bacteria-speciic characters and interactions between plants and bacteria. Some bacteria can produce not only all the hormones produced by plants (Friesen et al. 2011), but also other growth regulators, unusual for plants, which can afect plant morphogenesis and development. Vereecke et  al. (2000) reported that the supernatant of the culture medium of Rhodococcus fascians, which causes both in vivo and in vitro distortions within plants (galls, stem fasciation, brooms) contained 11 distinct cytokinins, which interfered with the metabolism of plants, including inluencing morphogenesis of in  vitro cultures. Rodestrine, a phytohormone with the properties of auxin, but not produced by plants, was obtained from the bacterium Rhodobacter sphaeroides (Sunayana et  al. 2005). Auxins that are produced by many bacteria afect the development of the root system, thereby enhancing the absorption of nutrients and water from the soil (Patten and Glick 2002). Bacteria both produce plant growth regulators, and stimulate the production and distribution of these compounds in plants (Vacheron et al. 2013). Cytokinins extend the period of leaf ability to assimilate, thereby increasing the amount of products of photosynthesis and replace plant cytokinins lost during drought conditions (Arkhipova et al. 2007). Giron et al. (2013) emphasized the role of bacterial cytokinins as key regulators of growth and defense processes. Bacterial gibberellins support elongation growth independently and in interaction with other hormones (Bottini et  al. 2004), and the ethylene level can be decreased by bacterial 1-aminocyclopropane-1-carboxylate (ACC) deaminase, thus reducing the susceptibility of plants to stress (Saleem et al. 2007; Saravanakumar 2012). Bacterial indole acetic acid (IAA) is known as an intermediary factor in shaping plant-microorganism interactions (Spaepen et al. 2007; Ludwig-Müller 2015b). Bacteria associated with disease resistance responses may also act as bio-control factors. Reduced susceptibility to pathogens may be related to the role of competitive colonization of tissues, or with antibiosis, consisting of disrupting the metabolism or degrading pathogens or pathogen toxins or virulence factors or by activating (priming) plant resistance (Compant et al. 2013). Bacteria have also been shown to protect plants before predators attack. Aballay et al. (2011) found that seven bacteria isolated from vineyards restricted the nematode population and the resulting damage to the in  vitro produced grapevine plants in a greenhouse experiment. Protection against abiotic stresses can result from exposure to substances that modify stress responses or stimulate the plant to activate metabolic responses associated with stress tolerance such as the production of osmoprotectants like glycine betaine or proline (Dimkpa et al. 2009; Grover et  al. 2011). For example, Burkholderia phytoirmans

Plant Cell Tiss Organ Cult

PsJN can adapt grapevine to cold by modiication of carbohydrate metabolism resembling natural cold acclimation (Fernandez et al. 2012) or/and by modiication of scavenging system (Theocharis et  al. 2012). Bacteria that provide protection against drought include Azospirillum brasilense (improved water status of wheat), Achromobacter piechaudii (ACC deaminase induced systemic tolerance of pepper and tomato), Bacillus megaterium (increased IAA and proline in Trifolium), Pseudomonas mendocina (increased lettuce resistance to drought by improving antioxidant status), Pseudomonas polymyxa (altered hormonal balance and stomatal conductance of Phaseolus vulgaris) (Grover et al. 2011). Rolli et  al. (2015) reported that three bacteria— Pseudomonas plecoglossicida, Acinetobacter calcoaceticus and Sphingobacterium canadense protected grapevine plants in the ield against drought. Pseudomonas luorescens YsS6 and P. migulae 8R6, produced ACC deaminase and signiicantly reduced the harmful efects of salinity in the cultivation of tomatoes (Ali et  al. 2014b) Among the common features of these bacteria is the production of IAA, the ability to dissolve phosphates, resistance to 20% PEG and the acceptance of a temperature in the range of 4 to 42 °C (Saravanakumar 2012). Bacteria can also afect plant metabolism by producing extracellular volatiles (Kanchiswamy et  al. 2015). For example Bacillus subtilis (GB03) produces volatile metabolites that in the long-term stimulate growth, the eiciency of photosynthesis, the accumulation of iron, and result in a greater seed yield in Arabidopsis thaliana (Xie et al. 2009). Volatiles of Bacillus badius M12 stimulated shoot regeneration from callus of Sesamum indicum, and increased the chlorophyll and carotenoid content, phenols and callus browning and induced organogenesis in tobacco callus (Gopinath et al. 2015). Zamioudis et al. (2013) showed that three strains of Pseudomonas spp. isolated from the rhizosphere had, in addition to providing protection against abiotic stressors and inducing a defense system against a number of pathogens, the ability to reprogram the mode of primary root growth in Arabidopsis thaliana. Endophytic bacteria can also participate in protection of plant photosystems against extreme environmental conditions through activation of a hormone dependent plant defense system and improving PSII electron transport (Burlak et al. 2013). Multi-efect microbial inluence on plants is sometimes called “priming”. In the primed state plants can respond more rapidly or/and efectively to a future stress (Goellner and Conrath 2008). Many endophytes exist in plants in a dormant state by maintaining a low metabolism, but they can resume the active state when environmental conditions change. Andreote et al. (2010) found that the endogenous bacterial population can be activated by the addition of beneicial bacteria to the growth environment. Ardanov et al. (2012)

reported that inoculation of potato plants with a strain of Methylobacterium induced the plant’s protection system against bacterial and fungal pathogens, with a force dependent on the cultivar and density of the pathogen inoculum. The Methylobacterium itself had no antagonistic activity against pathogens, but inoculation signiicantly changed the composition of the entire endophyte population in plant tissue, and thus increased the degree of resistance. This shows that the efect of bacteria introduced into plant tissue might also activate other pre-existing endophytes. However, it is not always clear whether accelerated growth or increased resistance is solely a result of bacterial metabolites, or also due to induction of the plant’s genetic apparatus by endophyte metabolites. According to Ludwig-Müller (2015a) plants and endophytes are equal partners in the production of secondary metabolites and can interact in the production of compounds and produce metabolites that are new to both organisms. For instance, Scherling et al. (2009) found that in tissue cultures of poplar inoculated with Paenibacillus sp. strain 22, 11 metabolites were changed in the plant, especially those related to the assimilation of nitrogen. Bacteria in plant tissue cultures For many years, the presence of bacteria in tissue culture was usually not disclosed in published manuscripts and was considered derogatory to a laboratory, as in  vitro cultures should be maintained in sterile conditions. However, over time it has become clear that despite surface sterilization of initial explants, cultures are not necessarily free from bacteria. The presence of some bacteria can be apparent in the initial stage, but at other times the contaminants may not be detected until the multiplication stage, and often even later when suboptimal conditions or acclimation may spur the growth of the bacteria. Contamination of plant explants, detection and elimination of contaminant bacteria were the focus of several reviews (Reed and Tanprasert 1995; Cassells 1997; Stead et al. 2000; Dunaeva and Osledkin 2015), including those in textbooks (Cassells 2011) but according to our knowledge there are no recent reviews concerning beneicial bacteria in plant tissue culture (Nowak 1998). Microorganisms in culture, even those that are nonpathogenic or not apparent, can have detrimental efects on the cultures and cause lack of multiplication or variation in experimental results (Tsao et al. 2000). Undetected bacteria can begin multiplying after a long period in culture. Pathogenic Xanthomonas axonapodis persisted as asymptomatic in anthurium shoot cultures for 1 year (Norman and Alvarez 1994) and pathogenic Agrobacterium vitis was able to persist in the latent stage within Vitis vinifera in vitro shoot cultures for 14 weeks (Poppenberger et al. 2002). There is much evidence that the interior of explants used for in vitro culture are colonized with a quantity of bacteria

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(Buckley et  al. 1995; Reed et  al. 1995; Reed and Tanprasert 1995). These are a combination of free-living bacteria, plant-inhabiting, animal-associated, but also those associated with processed food and sewage and even human pathogens (Cassells and Tahmatsidou 1996; Fletcher et al. 2013). Thomas et  al. (2007) found 14 isolates of bacteria belonging to nine genera, including those from human or animal related bacteria in 1 cm long shoot apices of papaya, prepared by surface sterilization. Some multiplied on the medium only in the presence of papaya shoots or extracts. De Almeida et  al. (2009) using an electron microscope, found bacterial endosymbionts inside cells of in vitro peach palm shoots considered axenic. Further analyses of DNA from these endosymbionts using PCR and denaturing gradient gel electrophoresis (DGGE) revealed the presence of three non-cultivable bacteria that showed similarity of rRNA sequences to Moraxella sp., Brevibacillus sp., and to a cyanobacterium. A similar molecular analysis by AbreuTerazi et  al. (2010) found bacterial endophytes belonging to Actinobacteria, Alphaproteobacteria and Betaproteobacteria in 5-year old axenic cultures of pineapple, sterilized supericially before DNA extraction. The authors observed diferences in the bacterial community within diferent plant organs. Lucero et  al. (2011) using microbiological, microscopic and nucleotide sequencing methods of identiication, found a rich microbiome consortium in regenerated leaves and roots of two Atriplex species that consisted of known and unknown bacteria and fungi. Fang and Hsu (2012) isolated bacteria of 13 genera from meristematic explants of six cultivars of Aglaonema; 30% of the colonies isolated were Pseudomonas aeruginosa. In a study of bacteria found in contaminated plant cultures obtained from several laboratories in Poland, 108 isolates in several genera were detected; with the most common being bacteria of the genera Bacillus, Methylobacterium and Pseudomonas (Kaluzna et  al. 2013). All isolates in this study, with the exception of Staphylococcus, were obtained from living explants, without disease symptoms. Although the bacteria are not always detectable, they may still have a negative impact on in vitro cultures (Thomas 2004b, 2011; Pirttilä et  al. 2008). For example, crypto bacteria Bacillus circulans, Sphingomonas paucimobilis Staphylococcus huminie and Micrococcus kristinae signiicantly decreased shoot proliferation in the shoot cultures of apricot (Marino et al. 1996). The above bacteria changed the medium composition, as well as the composition of the atmosphere in the vessels, which negatively inluenced culture growth. The habituation of plant tissue cultures has been known for decades and may be the result of bacterial contamination. Habituated cultures at a certain point in their growth can continue to grow without addition of exogenous plant growth regulators. Comparison of transcripts of habituated and non-habituated Arabidopsis thaliana cells showed

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various expressions of 800 genes, including up-regulation of genes coding for cytokinin receptors (Pischke et  al. 2006). In the light of more current knowledge of diicult to detect endophytic microorganisms, at least some cases of habituation can be considered the result of changing in auxin or cytokinin balance, possibly caused by endophyte metabolic activity. This is possible as indicated by indings that endophytes produce auxins, cytokinins, gibberellins and other plant hormones (Arshad and Frankenberger 1991; Lata et al. 2006; Weilharter et al. 2011). For bacteria non-pathogenic for ex-vitro grown plants but harmful for in-vitro explants Herman (1987) proposed the term “vitropaths”. Sterilization methods If pathogen-free donor plants are not available, sanitation protocols should be implemented. Removal or reduction of pathogens in donor plants may involve using fungicides, bactericides, antibiotics, and thermo- or chemotherapy followed by the isolation and culture of true meristems or the smallest possible shoot tips (Cassells and Doyle 2006; Cassells 2011). Shoot multiplication then should be carried out with culture lines derived from single initial explants. A broad spectrum and varying amounts of endophytic bacteria inhabit plants in  situ and eradicating all of them is practically impossible. Several methods of minimizing the contamination in plant tissue cultures were proposed (Reed and Tanprasert 1995; Bunn and Tan 2002). One of the most important is improving the phytosanitary condition of donor plants. Signiicantly fewer contaminations in the initial material are in donor plants growing in the greenhouse, watered to the substrate and preventively protected against bacteria and fungi (Leifert et al. 1994). Very important is a supericial surface sterilization that includes efective steriliants, their concentration and time, as well as the sequence of use. The most popular traditional biocides used are ethanol, calcium or sodium hypochlorite, mercuric chloride, hydrogen peroxide, and dichloroizocyanurates (Rowntree 2006; Cassells 2011), chlorine dioxide (Bhawana et  al. 2015) or nano silver (Abdi et  al. 2008). The eiciency of sterilization can increase if preparations are administered to explants through vacuum iniltration (Miyazaki et  al. 2010). For parts of donor plants that are dormant or for storage organs, a hot water treatment is recommended before explanting (Langens-Gerrits et al. 1997). Sometimes an inner sterilization, by means of forcing of shoots in 8-hydroxyqinoline-citrate (Szendrák et  al. 1997) or soaking in antibiotics (Falkiner 1997) or sulphonamide (Zenkteler et al. 1997) can reduce the number of bacteria. At this stage, when the nature of the bacteria is unknown, broad-spectrum antibiotics could be applied. Initial obviously contaminated explants should be discarded. All

Plant Cell Tiss Organ Cult

remaining viable explants should be repeatedly indexed, at least for the irst few subcultures to determine the presence of bacteria by incubation of basal fragments of explants on the microbiological liquid and semi-solid media and discarding those contaminated ones (Reed et  al. 1995; Reed and Tanprasert 1995; Thomas 2004a). Another possibility is a treatment of explants with biocides added to the culture medium, as sodium hypochlorite (Kohmura et  al. 1999), antibiotics (Reed et al. 1995, 1997; Falkiner 1997; Thomas et al. 2006), and other biocides such as PPM (Orlikowska et  al. 2012), Vitrofural (González-Olmedo et  al. 2005) or plant extracts (Marino et al. 2015). The antibiotic type and its concentration should be chosen on the basis of results of anti-biograms and having in mind that for plant cultures use, concentration should be further optimized. All types of biocides included in the growth medium should be irst tested for phytotoxicity to make sure that they are efective against the bacteria, and not detrimental to the explants (Buckley et al. 1995; Orlikowska et al. 2012). Even if the above measures are not successful for all bacteria, routine screenings followed by discarding contaminated cultures or applying biocides to a medium, cyclically repeated may allow a signiicant reduction of contaminations and enable the continuation of shoot propagation (Cassells 1991; Buckley et al. 1995).

Detection of bacteria The variety and amount of bacteria that occur naturally in plant tissues indicates why it is not practically possible to get completely clean plant explants. In the beginning of culture it is necessary and possible to remove bacteria that can easily multiply massively on plant media. They can be dangerous due to the ability to dominate over plant explants, isolating them from oxygen and competing for nutrition. A more diicult problem concerns bacteria that do not multiply on plant media. Some of them can be disclosed on bacteriological media if they are cultivable. Latent infections with pathogenic bacteria and covert contaminations with non-pathogenic types are the most troublesome. Unfortunately, only a few laboratories test explants for cultivable microorganisms. In addition, a testing procedure should be repeated to ensure that pathogenic microorganisms are not present at culture initiation and stabilization, during micropropagation and at acclimatization in the greenhouse. For optimal certainty, detection of pathogens in the initial explants and their ofspring should be carried out using extremely sensitive tests based on immunological or DNA markers, capable of detecting very small amounts of microbial DNA/RNA (Stead et al. 2000; James et al. 2014) with the best solution likely to be integrated tests (Alvarez 2004). These kinds of tests are especially needed for

disclosure of potentially pathogenic bacteria and several sensitive tests are currently in use. Some bacteria can remain in a hidden state (covert, cryptic) in plant tissues for many subcultures, appearing only when subjected to stress factors, resulting from changing the medium, prolonged passage, elevated temperature, or long-term storage at low temperatures (Leifert et  al. 1994; Thomas et  al. 2007). Some bacteria can multiply only in the presence of the plant tissue in which they dwell, i.e. Curtobacterium citreum in shoot culture of chrysanthemum (Panicker et al. 2007). These kinds of bacteria are diicult to ind and deine, because even molecular methods are sometimes not sensitive enough to detect such low amounts of bacterial DNA, especially when amplifying them together with prevalent amounts of plant DNA and with plant polymerase inhibitors, using PCR techniques. Pohjanen et  al. (2014) detected endophytes associated with tree meristems using in situ hybridization of bacterial DNA. Müller and Döring (2009) isolated particles visible in electron microscopy as bacteriosomes from plant cells, with the help of a 3-D micromanipulator and then studied their genomes independently of the plant DNA background. Bacteria can be also revealed with speciic staining and video imaging, recording their movements in the cytoplasm and periplasm. Some bacteria can be disclosed after biocide application, when is possible to diferentiate between them and other micro-particles in the cytoplasm (Thomas and Sekhar 2014). A disclosure of the uncultivable Methylobacterium sp. in potato explants grown in vitro was possible using molecular markers, but isolation was possible when its cultivability was increased in the efect of co-cultivation of cultures with Pseudomonas luorescens IMGB163 (Podolich et al. 2009). Efremova et  al. (2012) suggested that more knowledge concerning the presence of endophytic bacteria in plant tissues in  vitro might be available through protoplast or cell cultures. In this condition, microorganisms multiply, rapidly overgrowing the culture, often producing toxic metabolites resulting in the death of the cultures. A possible explanation is that the bacteria do not proliferate, or multiply to a very limited extent, if they are secured in their life niches in intact cells, but after removing the cell wall to obtain protoplast culture, or after breaking the connections between cells to obtain cell cultures, they reproduce and quickly become visible. Also Klocke et al. (2012) reported that endophytes hidden in the cells were able to multiply as a result of protoplast isolation. These and other examples of rapid disclosure of endophytes can be attributed to two factors—the appearance of a bacteria stressor (removal of the cell walls, the presence of cell wall degrading enzymes, elevated temperature or presence of other microorganisms), and/or host explants stressors that decrease host explants resistance (change of medium, including

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Plant Cell Tiss Organ Cult

growth regulators, the use of mutagenic agents, elevated or decreased temperature). In vitro applications of bacteria The symbiosis of bacteria with plants has prompted imitative use in plant production, including in vitro propagation. A spectacular example of the practical use of bacteria is the exploitation of Agrobacterium tumefaciens and A. rhizogenes. These soil bacteria, which cause pathogenesis in many plants, possess genetic equipment enabling colonization of plant cells. Since 1980, disarmed forms (deprived of tumorogenes) were used as vectors for transferring desirable genetic information (Păcurar et  al. 2011). Disarmed bacteria can introduce a speciic genetic construction to the nucleus or plastid of a plant. If this construction joins stably to the plant DNA, it can be transferred to daughter cells. Regeneration of whole plants from such “genetically enriched” cells lies at the base of transgenesis, and ofers an excellent source of new genetic variability that can be used in plant breeding (Ziemienowicz 2014). Numerous taxa of bacteria have been isolated from plant tissue cultures, and at least some of them displayed a possibility to increase plant growth rates or inluence morphogenesis in  vitro. In comparison to ex-vitro plant production, it is sometimes easier to adjust optimum conditions favoring the growth and organogenesis of explants during in vitro culture, for both research and industry. Genotypes that are recalcitrant or diicult in culture do not respond with efective regeneration, a high multiplication coeicient, or efective rooting. In this case, the inoculation of cultures with beneicial bacteria might help in overcoming the recalcitrance, by supporting cultures with growth regulators or other metabolites. For example, Rhodobacter sphaeroides produces the phytohormone rodestrine enhancing the rooting of mulberry microshoots (Sunayana et  al. 2005) and Bacillus spp. producing IAA promoted rooting of strawberry (Dias et  al. 2009). Quambusch et  al. (2014) found a link between endogenous bacteria and the eicacy of micropropagation of Prunus avium genotypes. Sometimes unexpected morphology or better quality of cultures may suggest the activity of endophytic bacteria. For example, elderberry cultures naturally contaminated with pink bacteria (Methylobacterium) formed fewer but longer axillary shoots when compared to non-contaminated ones. Raspberry shoots contaminated with a creamcolored bacterium were spiky and longer in comparison with those not contaminated. These and other bacteria were isolated and screened against rose, chrysanthemum, gerbera and hosta in vitro cultures. None of these bacteria were detrimental to the explants, and some combinations of bacteria/plant species signiicantly improved multiplication and rooting (Zawadzka et  al. 2014). In this study

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Curtobacterium increased shoot proliferation of all four plant species, as well as the rooting of rose; Methylobacterium increased productivity of gerbera and hosta while Bacillus lengthened shoots of chrysanthemums. The above and other examples of the beneicial impact of bacteria on in vitro cultures are listed in Table 1. The most important role of beneicial bacteria in the micropropagation industry is connected with acclimation of microplants, which is often a bottleneck of the process. The nonfunctional (open) stomata, not fully-functional roots and photosynthetic apparatus make the adaptation diicult for microplants in rapidly changing conditions. Inoculation of microplants at the last stage of propagation or at the weaning with beneicial bacteria could help overcome this challenge (Nowak 1998; Vestberg and Cassells 2009; Panigrahi et al. 2015). Bacteria belonging to 13 genera (Azorhizobium, Azospirillum, Azotobacter, Bacillus, Burkholderia, Curtobacterium, Enterobacter, Halomonas, Methylobacterium, Microbacterium, Methilophylus, Paenibacillus, Pseudomonas, Ralstonia, Rhodococcus, Rhodopseudomonas, and Sphingopyxis) caused positive impacts on micropropagation processes and in some instances possible mechanisms responsible for increased productivity were proposed. Bacteria stimulated shoot elongation, increased shoot weight, leaf number, axillary shoot growth, accelerated rooting, increased rate of rooted shoots, increased number and length of roots, induced somatic embryogenesis and helped in microplants’ acclimation to ex vitro conditions (Table 2). The special role of Burkholderia phytofirmans PsJN in micropropagation A group of Pseudomonas species (Bergey et al. 1984) were reclassiied as Brevundimonas based on phenotypic characterization, DNA-rRNA hybridization, protein patterns, and fatty acid composition (Segers et al. 1994). The genus Burkholderia includes more than 60 extremely variable species, inhabiting many life niches, and also acting as pathogens of humans, animals and plants (Suarez-Moreno et  al. 2012). Recently, all bacteria in this group, which are primarily environmental, were proposed to constitute a new genus Paraburkholderia gen. nov. (Sawana et al. 2014). Over 30 non-pathogenic Burkholderia species live in association with plants and can be considered potentially useful due to characteristics that can be beneicial for the host. These include the ability to convert atmospheric nitrogen into ammonia, provision of phosphorus and iron, production of growth regulators, protection against pathogens, and others (Compant et al. 2008b). Members of this genus are capable of supporting the growth of plants due to ACC deaminase and quinolinate phosphoribosyl transferase activity. Moreover, they can secrete into the environment siderophores,

From microbial collection

Azospirillum brasilense/Cd and Az39

Bacillus licheniformis/ R14M10 Pseudomonas luorescens R16M10

From roots and rhizosphere of On emerged roots Vitis vinifera

From spent alcohol used in subculturing of grapevine, residing as covert in explants From pelargonium seedlings On hypocotyl segments

Bacillus pumilus

Bacillus circulans

From rhizosphere

Azotobacter chroococcum/42

Azospirillum brasilense/Sp245 Surface of wheat roots

1. From microbial collection 2., 3. Locally isolated

1. Azospirillum brasilense/Cd 2. A. brasilense/Sp7 3. A. brasilense Az 39

Induced somatic embryogenesis in genotypes resistant for TDZ Increased shoot and root length, and leaf area, increased ABA and IAA level in leaves and roots, prevented water loss, induced mono- and sesquiterpene production

Larraburu and Llorente (2015)

Russo et al. (2008)

Andressen et al. (2009)

Thomas (2004b)

Murthy et al. (1999)

Salomon et al. (2014)

More eicient nutrient uptake

Assimilation of aerial nitrogen, IAA and PAA production, antimicrobial activity

NA

NA

NA

Production of ABA, IAA, GA1 and GA3

Carletti et al. (1998) Larraburu et al. (2007) Gonzalez et al. (2015)

On shoot base of Simmondsia Increased root number chinensis before rooting On microshoots of Photinia × Accelerated rooting, increased fraseri before rooting shoot and root fresh and dry weight and root surface area; increased salt tolerance On shoots bases of Handroan- Increased % of rooted shoots, length of shoots and roots thus impetiginosus after root number, decreased auxin induction requirement Accelerated rooting, increased Before or after rooting on number, length and weight shoot base of Prunus cerasof roots, number of nodes, ifera Mr.S 2/5 length and weight of shoots; during rooting and acclimatization, protection of microshoots for Rhizoctonia spp Increased number of axillary On bases of shoots of Simshoots mondsia chinensis before rooting On microshoots of grape Increased number and weight before rooting of roots; accelerated rooting

From microbial collection

Parray et al. (2015)

Authors

Excretion of plant growth regulators Replacement of exogenous auxin; resistance for salt

1., -3.-6. IAA production On 30–70 day-old-cormlets of 1., 2., 4. 100% cormlet ger2.-6. Siderophore production Crocus sativus mination 3.-5. Increased cormlet weight 1.-6. Phosphate solubilization 3. + 4. + 5. Increased cormlet proliferation

From safron rhizosphere

The impact mechanism

1. Acintobacter lwoi 2. A.haemolyticus 3. Bacillus subtilis 4. Klebsiella sp 5. Pantoea sp 6. Pseudomonas sp Azospirillum brasilense/Cd

Type of action

Subject of inoculation

Source

Taxon/strain

Table 1 Taxon, source, action and impact of bacteria used in bacterization on in vitro plant cultures

Plant Cell Tiss Organ Cult

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13 On nodal explants of potato

From roots of onion

As above

As above

As above

As above

From vineyard soil

From in vitro cultures of chry- Persistent contamination santhemum covert-type in chrysanthemum culture On shoot bases before rooting 1. and 2. From contaminated of chrysanthemum, gerbera, raspberry cultures hosta and rose (shoot tips 3. From contaminated hosta were used for multiplication cultures studies)

From shoots of sugar canes

Rhizosphere of Equisetum debile

Burkholderia phytoirmans /PsJN™ (earlier Pseudomonas sp. /PsJN)

As above

As above

As above

As above

Burkholderia spp. IF25

Curtobacterium citreum (3 morphotypes)

1. Curtobacterium pusillum 2. Methylobacterium extorquens 3. Paenibacillus glucanolyticus

Enterobacter sp. /SC20

Halomonas desiderata /RE1

On rooted shoots of Saccharum oicinarum Inoculation of germinated seeds, internodal explants and callus of Brassica oleracea

On bases of microcuttings

On rooted shoots of potato

On weaned seedling roots of Panicum virgatum On the base of microshoots in rooting medium of Helleborus sp

On nodal segments of Vitis vinifera

Subject of inoculation

Source

Taxon/strain

Table 1 (continued)

1. Increased number of axillary shoots, number and length of rose roots 2. Increased number and length of shoots and roots gerbera and hosta, number of shots of chrysanthemum 3. Increased number and length of chrysanthemum shoots and length of chrysanthemum roots Increased dry weight of shoots and roots Increase in shoot length, adventitious shoots and callus proliferation depending on supernatant concentration and explants type

Stimulated microshoots growth; increased roots number, dry weight of shoots and roots, stimulated cuticular hairs on leaves, secondary roots and ligniication Increased shoot length, number of nodes, dry weight of shoots and rots and overall biomass microplants, protected of shoot explants against Botritis cinerea Increased shoot and root growth, of Alamo cv Increased number of rooted shoots, number and length of roots and acclimatization at non-optimal temperature Increased fresh weight of microplants Fastened rooting, increased roots number Increased number of axillary shoots

Type of action

Assimilation of aerial nitrogen, production of IAA Salt tolerance, IAA production

1.-3.Assimilation of aerial nitrogen 2., 3. IAA production

Change in amount of IAA, trans-zeatin and GA3 Modulation of auxin biosynthesis Replacement of BAP and kinetin

Ali and Hasnain (2007)

Mirza et al. (2001)

Zawadzka et al. (2014)

Panicker et al. (2007)

Muganu et al. (2015)

Kurepin et al. (2015)

Orlikowska et al. (2017)

NA

Barka et al. (2000)

Inhibition of Botritis cinerea on PDA medium

Kim et al. (2012)

Frommel et al. (1991)

Production of plant hormones

NA

Authors

The impact mechanism

Plant Cell Tiss Organ Cult

Source

NA not available

On oregano microshoots

From soybean

Pseudomonas mucidolens, P. sp./ATCC 31461 Not identiied

From in vitro cultures of Pinus On hypocotyl bases of Pinus elliotti elliotti after cut of roots

On base of raspberry shoots

As above

As above

On base of oregano shoots

From contaminated oregano cultures

On bases of shoots diicult to propagate Prunus avium genotypes On the bases of populus microshoots bases Co-cultivation of soybean calli for 45 days Added to rooting medium to MILCAP substrate On nodal segments of Mentha piperita Increased number and length of roots Induced nodular calli followed by somatic embryos Promoted growth of Primula roots 2.-4. increased shoot fresh and dry weight 1.-4. Increased ramiication 4. increased leaf number 1., 2., 4. Increased essential oils yield Prevented hyperhydricity of oregano explants, increased content of phenolics and chlorophyll Prevented hyperhydricity of raspberry cultures Prevented hyperhydricity of oregano cultures Enabled rooting and acclimatization of seedlings

Quambush et al. (2014)

Kalyaeva et al. (2003)

Authors

Santoro et al. (2015)

Shetty et al. (1995)

1.-3. production of IAA 1., 4.siderophore production, 1.-4. phosphate solubilisation

Production of extracellular polysaccharides

NA

Burns and Schwarz (1996)

Ueno and Shetty (1997)

Ueno et al. (1998)

Digat et al. (1987)

NA

Production of extracellular polysaccharides As above

Yang et al. (1991)

NA

Assimilation of aerial nitrogen Ulrich et al. (2008)

1., 3. Stimulated formation of Production of IAA and cytokinins morphogenic calli 2., 4. Stimulated development of primary shoots 3. Stimulated formation of morphogenic calli and shoot regeneration Increased % of rooting and NA number of roots

On immature embryos

The impact mechanism

Type of action

Subject of inoculation

Pseudomonas sp./F

1. Methylobacterium sp. /D10 In order: from soil, from maize rhizosphere, from rice 2. Methylovorus mays /VKM rhizosphere, or sewage V-2221 3. Methyloilus glucoseoxidans /B VKM V-1607 4. Methilophylus methylotrophus /VKM V-1623 From contaminated explants Microbacterium testaceum of easy for micropropagation /D-1-1 Prunus genotype Rhodopseudomonas sp./N-1-2 Paenibacillus humicus/P22 From contamination of Populus cultures Pseudomonas maltophilia/ From contaminated soybean PmSoy1 cultures Unknown Pseudomonas putida/G-92 and P. luorescens/L 26-1 From rhizospere of ield Pseudomonas putida grown Mentha plants 1. /SJ04 2. /SJ25 3. /SJ48 4. P. luorescens WC5417r

Taxon/strain

Table 1 (continued)

Plant Cell Tiss Organ Cult

13

Source

13

Paenibacillus macerans

Enterobacter sp./SC20

1. Bacillus sp./CaB5 2. Pseudomonas luorescens/ R68 3. Pseudomonas putida/ R79

Bacillus subtilis Bacillus sp Pseudomonas corrugata Bacillus, consortium of 3 strains/INR7/T4/IN 937b

Type of action

Protected microshoots for On shoot base of Prunus cerasifera Mr. S 2/5 before or Rhizoctonia spp. during rooting and acclimatization after rooting Facilitated acclimatization, On bases of microshoots of increased shoots length and rootstocks Mr.S2/5 (Prunus nodes number cerasifera x P. spinosa), GF 677 (P. persica x P. amygdalus) after rooting Mixed with substrate for accli- Increased survival rate, shoot matization of tee microplants length, root number, fresh weight, protected before pathogenic wilting On rooted plantlets Increased number and weight of roots and shoots in ex vitro tests

Subject of inoculation

To the substrate at planting of microshooots of Picrorhiza kurrooa

Increased % of survival, length of shoots and roots, plant biomass and P content in shoots and roots From rhizosphere of tea plants To growth substrate at planting Enhanced survival of microof tea microplants plants, increased shoot length and leaves number 20 days after transplanting Increased fresh and dry From microbial collection banana plantlets to trays weight, pseudostem diam(presumably from rhizoseter, foliar surface and conphere) tents of N, P, K in leaves 4× to the substrate for microIncreased leaf number and From rhizosphere propagated banana size, height of plants, num1. Capsicum annuum 2.Sizygber and length of roots, fresh ium jambos weight of shoots and roots; 3. Phyllanthus amarus reduced hardening period From shoots of sugar canes On rooted shoots of SacchaIncreased dry weight of shoots rum oicinarum and roots Increased number, length From meristems of Cymbidium On the microshoot bases of and dry weight of roots and eburneum Cattleya loddigestii at the number of leaves acclimatization stage in the greenhouse

From spent alcohol used for subculturing of grapevine shoots, existing as cover in shoots From bacterial collection

Bacillus pumilus

Bacillus megaterium Bacillus subtilis Pseudomonas corrugata

From soil of tea plantation

Azospirillum spp

Azospirillum brasilense/Sp245 As above

Azospirillum brasilense/Sp245 From surface of wheat roots

Taxon/strain

Table 2 Taxon, source, action and impact of bacteria used in bacterization on acclimatization of microplants to ex vitro conditions

Russo et al. (2008)

Assimilation of aerial nitrogen, IAA and PAA production, antimicrobial activity As above

Trivedi and Pandey (2007)

Jaizme-Vega et al. (2004)

Suada et al. (2015)

Antifungal activity against fungi isolated from plants during acclimatization in in vitro tests Antifungal activity against pathogens of tea in in vitro tests NA

NA

Assimilation of aerial nitrogen, production of IAA Production of indole compounds

Thomas (2004b)

NA

Faria et al. (2013)

Mirza et al. (2001)

Pandey et al. (2000)

Thomas et al. (2010)

Higher activity of defense enzymes, nitrogen ixation

Vettori et al. (2010)

Authors

The impact mechanism

Plant Cell Tiss Organ Cult

NA not available

Not identiied (RB)

Rhizobium 7 strains

Pseudomonas mucidolens/ ATCC 4685 P. sp./ATCC 31461

Pseudomonas sp./F

Pseudomonas luorescens/ CHA0 and IP10

From rhizosphere (microbial collections)

On microcuttings of potato and Increased stem length, rooting eiciency and survival in the strawberry as a spray with greenhouse and increased Pseudomonas irst then with resistance against Erwinia Mehylovorus carotovora, Sclerotinia sclerotiorum and Phytophthora infestans From potato tubers On potato microplants before Increased plant survival at acclimatization acclimatization, fresh weight of shoots and number and weight of tubers (IP10) and shoot growth (CHA0); protected against Rhizoctonia solani From contaminated oregano On base of raspberry shoots Increased % of acclimatized tissue cultures microplants, decreased water content and phenolic compounds From bacterial collection On oregano microshoots Increased % of acclimatized (presumably from soil) microplants, increased content of chlorophyll, phenolic compounds and dry weight, decreased fresh weight Increased survival rate and From root nodules of Robinia On the top of soil before pseudocaccia plantlets of R. pseudoacaccia growth rate, depending on strain transplantation From in vitro cultures of Pinus On hypocotyls base of Pinus Enabled acclimatization of elliotti elliotti after cut of roots seedlings

Type of action

1. Pseudomonas aureofaciens BS 1393 2.Methylovorus mays/VKM B-2221

Subject of inoculation

Source

Taxon/strain

Table 2 (continued)

Dufy et al. (1999)

Ueno et al. (1998)

Ueno and Shetty (1997)

Balla et al. (1998)

NA

Production of extracellular polysaccharides

Production of extracellular polysaccharides

NA

Burns and Schwarz (1996)

Zakharchenko et al. (2011)

Solubilization of phosphates and secretion of active substances with fungistatic action

NA

Authors

The impact mechanism

Plant Cell Tiss Organ Cult

13

Plant Cell Tiss Organ Cult

antibiotics, protective elicitors, such as polysaccharides, and activate induced systemic resistance in plants (SuarezMoreno et al. 2012). Burkholderia spp. colonize the outer and inner plant tissues and are endosymbionts of many plant species. Some strains are predators of pathogenic microorganisms, which make them potential candidates for bio-protection (Cain et al. 2000). Due to these unique characteristics, the search for Burkholderia isolates is ongoing (Young et  al. 2013). B. phytoirmans strain PsJN, isolated from onion roots inhabited by mycorrhizal fungi (Frommel et  al. 1991) is the most widely described bacterium having a beneicial efect on plants for both ex vitro and in  vivo propagation and growth. It was initially classiied based on biochemical and physiological traits as a non-luorescent pseudomonad and named Pseudomonas sp strain PsJN (after its discoverer Dr. Jerzy Nowak). According to sequence analysis of the 16S rRNA it was renamed as B. phytoirmans (Mitter et  al. 2013). It became a model for studying bacterization in plant tissue culture (Bordiec et al. 2011; Poupin et al. 2013; Lara-Chavez et al. 2015). B. phytoirmans strain PsJN can colonize several plants species, positively afecting their growth and wellness, initially colonizing the roots before moving onto the aerial parts (Compant et  al. 2008b). Several species responded positively to colonization with this bacterium, for example Arabidopsis thaliana (Poupin et  al. 2013), maize (Naveed et al. 2014b), switchgrass (Kim et al. 2012) and Helleborus (Orlikowska et  al. 2017). The growth promotion in potato (Conn et  al. 1997; Kurepin et  al. 2015) and in switchgrass was cultivar speciic (Kim et al. 2012). Interestingly, Kurepin et al. (2015) found that after inoculation of potato with PsJN, a slower growing cultivar matched the growth rate of the rapidly growing cultivar, and that growth was accompanied by an increase GA3 and reduction of transzeatin in the slow growing cultivar. This indicates that the interaction of bacteria and plant is associated with the biosynthesis of plant growth regulators. PsJN inhibited colonization of in  vitro grapevine cultures by Botrytis cinerea (Barka et  al. 2002) and tomato by Verticillium dahliae (Sharma and Nowak 1998). Colonization with B. phytoirmans increased resistance of plants to non-optimal growth temperatures—low in grapevine (Theocharis et  al. 2012) and high in potato (Bensalim et  al. 1998). Arabidopsis thaliana colonized by PsJN was less susceptible to plasmalemma disruption under freezing stress (Su et al. 2015). Colonization of Helleborus microshoots with this bacterium showed better growth under non-optimal temperatures (23 vs. 15 °C) (Orlikowska et  al. 2017). Wheat (Naveed et al. 2014a) and maize (Naveed et al. 2014c) plants from seeds inoculated with PsJN were less sensitive to drought stress under ield conditions than those not inoculated. Poupin et  al. (2013) determined that B. phytoirmans PsJN when inoculated into germinated seeds of Arabidopsis

13

thaliana, inluenced the plant throughout the complete growth cycle. It initially stimulated vegetative growth, then accelerated the development of generative organs, and thus shortened the life cycle. Transcriptome analysis of inoculated plants showed that 364 genes were over expressed and 282 genes were under expressed, when compared to noninoculated plants. Zhao et al. (2016) revealed in PsJN inoculated Arabidopsis seedlings expression of genes related to iron storage, siderophore biosynthesis and transport, as well as higher absorption minerals Fe, Zn and Cr, which can contribute to plant growth promotion and alteration of metabolites (Su et  al. 2016). PsJN has a large genome, unlike other endophytic bacteria. This may have resulted in the presence of a large number of genes encoding a number of physiological functions that enable its endophytic behavior (Mitter et al. 2013). Ali et al. (2014a) demonstrated by means of comparative genomic analysis of several endophytes, that B. phytoirmans has all the genes of nine other bacteria studied, related to transportation, secretion, degradation of polymers, regulation of transcription, detoxiication, stabilizing redox potential that help in the efective colonization, as well as the establishment of positive interactions with host plants. According to Mitter et al. (2013) the ability of PsJN to colonize plants and to establish an endophytic relationship resulting in a beneicial inluence on unrelated plants, is the efect of the bacterial genes coding for such metabolites as siderophores that improves iron assimilation, poly-3-hydroxybutyrate than overcomes carbon starvation, heavy metal and drug resistance, unfavorable compound degradation and other characteristics that enable bacteria to adapt to diferent conditions. Park and Lazarovits (2014) obtained results suggesting that plant growth enhancement after inoculation with PsJN can be the result of more eicient sugar uptake through direct or indirect stimulation of hexokinase1 activity. B. phytoirmans PsJN has a genetic equipment to produce IAA and that allows it to be involved in plant growth and root proliferation. It also has the operon involved in a degradation of IAA what was suggested as a factor enabling root colonization (Zúñiga et  al. 2013). Despite the sequencing of the entire genome of B. phytoirmans PsJN, most of its functions, especially those related to the interaction with plant genes are not yet explained (Sessitsch et al. 2005). Despite the ability to colonize many plant species and repeatedly proven beneicial impact on several plants, level of growth promotion by PsJN is cultivar speciic (Conn et al. 1997). In vitro and ex vitro bacterization/biotization of micropropagated plants It is reasonable to use some bacteria for supporting plant growth and resistance in biofertilization or bioprotection, in

Plant Cell Tiss Organ Cult

order to reduce the use of mineral fertilizers and pesticides in agriculture. Bacterization can be particularly meaningful in organic plant production. Many microorganisms were found to be beneicial for plants, but their efectiveness in the ield was not conirmed in the ield trials or ield trials were not conducted (Owen et  al. 2015). The efectiveness of preparations based on living organisms and provided for living organisms is very dependent on environmental conditions. Especially diicult is maintaining a high bacterial population in the soil during the time of plant colonization. Research should include the highest concern for searching for more efective bacteria, including genetically engineered, better formulated, resistant to sub-optimal environmental conditions, and consortia of microorganisms, which will mimic at least partly, the natural plant microbiome that is numerous, multispecies and multifunctional, as well as for positively reacting cultivars (Owen et al. 2015). A history of bacterial inoculation on the background of contemporary knowledge was reviewed earlier (Bashan 1998; Bashan et al. 2014). The idea of an application of bacteria to improve the efectiveness of micropropagation emerged more than three decades ago. The possibility of improving the eiciency of plant tissue cultures with the aid of some bacterial “contaminators” was originally suggested by Herman (Herman 1987, 1990). The result of bacterization of plant cultures in  vitro was at irst reported by Digat et  al. (1987), who discovered the positive inluence of Pseudomonas luorescens and P. putida strains on the rooting and acclimatization of primula microshoots. Subsequent reports showed the beneicial efect of Pseudomonas sp. and P. mucidolens in avoiding hyperhydricity in oregano and raspberry cultures (Shetty et al. 1995; Ueno et al. 1998). Nowak (1998) reviewed the idea of bacterization of in vitro explants quoting a number of beneicial efects caused by some bacteria on in  vitro cultures, emphasizing beneits on post in-vitro growth. The microplants are exposed to high stress after being transferred to ex vitro conditions, when they must become autotrophic organisms. At this time, poor development of vascular and covering tissues and a lack of functional roots, dryness of leaves, photo-inhibition caused by excessive exposure to the sun in the absence of a matured photosynthetic apparatus, and infections by pathogenic microorganisms are all real threats. Beneicial bacteria may help in the ight against stress, not only by providing growth regulators, facilitating nutrient uptake and direct or indirect protection against stresses, but also through initiating microplant defense responses in the process of biohardening or priming (Nowak and Shulaev 2003; Chandra et  al. 2010; Panigrahi et  al. 2015). This process was described broadly in potato cultures (Nowak et  al. 1999). Compant et  al. (2005) noted that the beneicial bacteria used when inoculating explants at the in vitro stage, could

stimulate the induction of defense processes, which may be crucial in overcoming transplanting stress. Although technically, biotization of explants during in  vitro culture is relatively easy, some condition parameters such as inoculation density and temperature should be met (Pillay and Nowak 1997; Ardanov et al. 2011). As was mentioned above, bacterization is not always rational at the in vitro stage of propagation, but may be more appropriate for the acclimatization, and added at weaning, after delasking, to the naked roots or the growth substrate. Several examples illustrating the role of bacterization in acclimatization are given in Table  2. They include Rhizobium for Robinia (Balla et al. 1998) or Bacillus for banana (JaizmeVega et al. 2004; Suada et al. 2015), Efect of bacterization before or during acclimatization can be maintained also during the ield cultivation, positively inluencing growth and yielding of plants by the constant presence of bacteria in plants or by the activation of defensive processes initiated in the previous growth stage (priming) (Table 3). Although it is easier to perform bacterization on explants at the stage of in vitro cultures, it may be not preferable in all cases. Thomas et al. (2010) found that inoculation at the in vitro rooting stage of tea microshoots with Pseudomonas luorescens and Azospirillum brasilense isolated from tea plants was not efective, as the irst one did not colonize and the second one overgrew the cultures and inhibited the growth of shoots. However, when these bacteria were added to the substrate during acclimatization in the greenhouse they increased survival by 30% for Pseudomonas luorescens and 60% for Azospirillum brasilense and stimulated growth of roots and shoots. The advantage of using bacteria for growth promotion and priming for resistance against stresses still depends on the genotypes of bacteria and the host plants and the growing conditions, for both in vitro as well as in vivo conditions. In vitro cultures as a useful model for studying efects of bacteria on plants The ease of bacterial application and deining the plant response in vitro are factors to consider in the pre-selection of suitable microorganisms as bioprotectors or biofertilizers to apply in the ield. The impact of Burkholderia phytoirmans PsJN on the ability of in vitro grapevine cultures to resist low temperatures (4 °C) was studied using as a markers the weight of roots (Barka et al. 2006), activity of scavenging system (Theocharis et  al. 2012), and carbohydrate metabolism (Fernandez et  al. 2012). Sensitivity of potato to high temperatures (33/25 °C), was decreased by PsJN and expressed by increased stem length, shoot and root biomass and stronger tuberization post in  vitro (Bensalim et al. 1998). Gonzalez et al. (2015) stated that jojoba microshoots inoculated in  vitro with Azospirillum brasilense

13

13

As above

From shoots of sugar canes

1. From microbial collection 2. From rhizosphere of papaya

As above

Enterobacter sp./SC20

1. Gluconoacetobacter diazotrophicus PAL 5 2. Diazotroph Pachaz 008

NA not available

As above

From meristems of 3 strawberry cultivars propagated in vitro From onion roots

Bacillus subtilis—7 strains Sphingopyxis sp.

As above

From diseased wheat seeds

Bacillus subtilis DAR26659

As above

1. From microbial collection 2., 3. Locally isolated

1. Azospirillum brasilense/Cd 2. A. brasilense/Sp7 3. A. brasilense/Az 39

Burkholderia phytoirmans/ PsJN™ (earlier Pseudomonas sp./PsJN) As above

Inoculated on embryogenic callus of rice

From stem nodules of Aeschynomene aspera

Azorhizobium caulinodans/ ORS 571

Type of action

Increased length of shoots, weight of biomass and number of grains Before rooting of Photinia × Better adaptation to in vivo fraseri conditions; accelerated leaves development, stimulated the thickening of the cuticle and elongation of the hair root zone Reduced disease incidence, On fully acclimatized microincreased fresh and dry plants of ginseng planted weight of shoots and rhiin the soil infected with F. zomes oxysporum f. sp. zingiberi On base of strawberry microIncreased number and length of shoots roots, dry matter of roots and shoots and number of leaves On tomato plantlets sensitive Protected plants in greenhouse for Verticillium dahliae during early growth stage (5 months) against V. dahliae On nodal explants of 18 potato Promoted growth of 10 potato clones breeding clones, increased shoot length and biomass weight of shoots and roots, tuber number and weight On weaned seedling roots of Increased shoot and root Panicum virgatum biomasses, accelerated tillering. The growth stimulation difered with genotypes On germinating Arabidopsis Increased fresh weight of seeds 14-day old seedlings, number of hair roots, content of chlorophyll and leaves surface, accelerated tillering On rooted shoots of Saccharum Increased dry weight of shoots oicinarum and roots On roots of pre-hardened 1. Increased plants height Agave tequilana plants 2. Increased stem diameter

Subject of inoculation

Source

Taxon/strain

Table 3 Taxon, source, action and impact of bacteria used in bacterization of microplants on the plant ield performance

Senthilkumar et al. (2008)

Larraburu et al. (2010)

Rames et al. (2009)

Dias et al. (2009)

Sharma and Nowak (1998)

Bensalim et al. (1998)

Kim et al. (2012)

Nitrogenase activity

Development of microaggregates around roots (7-yearold trees)

Ability to lyse fungal hyphae

Solubility of phosphates and IAA production NA

NA

NA

Assimilation of aerial nitrogen, Mirza et al. (2001) production of IAA Nutritional and hormonal Ruiz et al. (2011) support

Activates 408 genes, including Poupin et al. (2013) those connected with auxin and gibberellin metabolism and with stress response

Authors

The impact mechanism

Plant Cell Tiss Organ Cult

Plant Cell Tiss Organ Cult

were less sensitive to NaCl in the medium as expressed by rooting ability. B. phytoirmans PsJN inoculated on vitro microshoots of grapevine protected cultures against grey mold indicating its usability in the ield. Rakotoniriana et al. (2013) tested in vitro a possibility to protect Centella asiatica against Colletotrichum higginsianum with the aid of Bacillus subtilis BCA31. (See also Table 3). In vitro cultures were used to study the potency of bacteria as biofertilizers in several instances. Wang et  al. (2015) tested in  vitro inluence of PsJN on switchgrass and revealed that inoculated seedlings had higher biomass, which constitutes very good indication for the use of this bacterium in ield production. Guglielmetti et  al. (2013) tested the in vitro efect of Luteibacter rhizovicinus MIMR1, producing IAA and molecules chelating iron ions, and dissolving calcium phosphate on root growth of barley seedlings and found that it was a good candidate to apply as a bio-fertilizer component. Montañez et  al. (2012) and Naveed et  al. (2014b), conirmed that the method using in  vitro culture in testing usefulness of bacteria for maize growth promotion can be used for preselecting bacteria for their use as bio-inoculants under ield conditions.

Conclusions One of the reasons for the propagation of plants under in vitro conditions is that the planting material produced is free from diseases and pests. The use of sterile technique during in vitro propagation ensures that uninfected explants introduced into culture, are likely to remain so. For this reason, an important and obligatory element of the initial step is to verify that pathogenic microorganisms (fungi, bacteria, phytoplasma, viruses and viroids) are not present in the donor plants (Reed and Tanprasert 1995). There is a common belief that the total (hypothetical) elimination of bacteria from plant tissues would cause signiicant changes in the phenotype of plants in terms of morphological and functional features (Rosenblueth and Martinez-Romero 2006; de Almeida et  al. 2009). Due to the undetected bacteria present in plant tissues, the term “axenic” (explants free of all biological contaminations) can not be used. Instead, the term “aseptic” (free of detectable contamination) is best used for properly maintained plants in vitro cultures (Cassells 2011) that are free of pathogens and visible contaminants and are periodically tested for cultivable microbiota. Pathogenic bacteria and those that easily multiply on plant media should be strictly prohibited from in vitro cultures. The others should be detected through routine bacteriological indexing and removed (Reed et  al. 1995). In addition to the removal of pathogenic and contaminating bacteria, positive attention

should be paid to those bacteria that can be helpful in micropropagation. Partida-Martinez and Heil (2011) propose that plants and their inhabiting bacteria form “super-organisms” that should be treated as an ecosystem. The interaction between plant and endophytic bacteria can range from commensalism to mutualism or switch to antagonism under certain conditions. Bacteria can inluence plants through molecular signaling, modulation of host hormonal balance, modiication of plant nutrition, and priming for tolerance of stresses, thus increasing plant productivity (Hardoim et  al. 2015). Plants also inluence the number, diversity and activity of microorganisms in the rhizosphere as well as those that inhabit the tissues endophytically (Vacheron et  al. 2013). Given the myriad of microorganisms living in the environment that may afect the plant and each other, many unknowns can be expected regarding their interactions. To better understand this world, it is necessary use more eicient methods, such as next-generation (high-throughput) sequencing technologies (NGS) (Mendes et  al. 2011; Knief 2014) for the identiication of microbiomes and genes involved in these interactions. These technologies are now more available and afordable than earlier sequencing methodologies. The multiplicity and diversity of bacteria provoke scientists to study interactions of plant microbes for practical use in agriculture. This has been realized for years in the form of commercial preparations containing beneicial bacteria. It would be naive to hope that single microorganisms or a limited number of microorganisms organized in consortia will improve wellness of a diverse range of plants grown in varied environmental conditions. Therefore their success mostly depends on plant type, place of growth and vegetation season. Nevertheless, the most beneits should be expected from situations where plants grow in suboptimal or poor conditions. There are several examples indicating that intentional inoculation of cultures with growth promoting bacteria can signiicantly improve in  vitro propagation, adventitious organogenesis or embryogenesis, but many more reports show the beneicial role of inoculation with those bacteria for acclimatization of microplants to ex vitro conditions (Chandra et al. 2010). A supplementation of microplants with selected bacteria can help to re-establish at least partly the ex vitro microbiome and thus protect young plants before the stresses that accompany acclimatization. Although interaction of some beneicial endophytic bacteria with some plant hosts are partially deined and some are practically exploited, the relationship of these bacteria with other microorganisms living on and in the plant and in the rhizosphere remains largely unknown in most cases (Compant et al. 2013) and therefore their inluence is not always repeatable and even can be unpredictable.

13

Plant Cell Tiss Organ Cult

Bacterization of microcuttings or microplants during in vitro culture is relatively easy and allows better control of the colonization process during the rooting on solid or in liquid medium or upon transfer to a greenhouse in a sterile substrate. On the other hand, the efect of bacterization is of less importance for in vitro stages, since the conditions for growth are generally suitable. Keeping in mind that endophytic bacteria reveal their full beneicial impact on plants growing in adverse conditions (Lowman et al. 2015), their use for in vitro cultures is not always necessary due to the ease of optimizing the in  vitro conditions by other means but it can be beneicial in the acclimated plant. Author contributions TO conceived the project and did most of the writing with emphasis on beneicial bacteria, KN collected and analyzed the literature, BR assisted with literature analysis, writing with emphasis on contamination, reference management and editing. Compliance with ethical standards Conlict of interest of interest.

The authors declare that they have no conlict

References Aballay E, Mårtensson A, Persson P (2011) Screening of rhizosphere bacteria from grapevine for their suppressive efect on Xiphinema index Thorne & Allen on in vitro grape plants. Plant Soil 347:313–325. doi:10.1007/s11104-011-0851-6 Abdi G, Salehi H, Khosh-Khui M (2008) Nano silver: a novel nanomaterial for removal of bacterial contaminants in valerian (Valeriana oicinalis L.) tissue culture. Acta Physiol Plant 30:709–714. doi:10.1007/s11738-008-0169-z Abreu-Tarazi MF, Navarrete AA, Andreote FD, Almeida CV, Tsai SM, Almeida M (2010) Endophytic bacteria in long-term in  vitro cultivated “axenic” pineapple microplants revealed by PCR–DGGE. World J Microbiol Biotechnol 26:555–560. doi:10.1007/s11274-009-0191-3 Ali B, Hasnain S (2007) Eicacy of bacterial auxin on in vitro growth of Brassica oleracea L. World J Microbiol Biotechnol 23:779– 784. doi:10.1007/s11274-006-9297-z Ali S, Charles TC, Glick BR (2014a) Amelioration of high salinity stress damage by plant growth-promoting bacterial endophytes that contain ACC deaminase. Plant Physiol Biochem 80:160– 167. doi:10.1016/j.plaphy.2014.04.003 Ali S, Duan J, Charles TC, Glick BR (2014b) A bioinformatics approach to the determination of genes involved in endophytic behavior in Burkholderia spp. J Theor Biol 343:193–198. doi:10.1016/j.jtbi.2013.10.007 Alvarez AM (2004) Integrated approaches for detection of plant pathogenic bacteria and diagnosis of bacterial diseases. Annu Rev Phytopathol 42:339–366. doi:10.1146/annurev. phyto.42.040803.140329 Andreote FD, da Rocha UN, Araújo WL, Azevedo JL, van Overbeek LS (2010) Efect of bacterial inoculation, plant genotype and developmental stage on root-associated and endophytic bacterial

13

communities in potato (Solanum tuberosum). Antonie Van Leeuwenhoek 97:389–399. doi:10.1007/s10482-010-9421-9 Andressen D, Manoochehri I, Carletti S, Llorente B, Tacoronte M, Vielma M l (2009) Optimization of the in  vitro proliferation of jojoba (Simmondsia chinensis (Link)Schn.) by using rotable central composite design and inoculation with rhizobacteria. Bioagro 21:41–48 Ardanov P, Leonid O, Iryna Z, Natalia K, Maria PA (2011) Endophytic bacteria enhancing growth and disease resistance of potato (Solanum tuberosum L.). Biol Control 56:43–49. doi:10.1016/j.biocontrol.2010.09.014 Ardanov P, Sessitsch A, Häggman H, Kozyrovska N, Pirttilä AM (2012) Methylobacterium-induced endophyte community changes correspond with protection of plants against pathogen attack. PLoS ONE 7:e46802. doi:10.1371/journal. pone.0046802 Arkhipova TN, Prinsen E, Veselov SU, Martinenko EV, Melentiev AI, Kudoyarova GR (2007) Cytokinin producing bacteria enhance plant growth in drying soil. Plant Soil 292:305–315. doi:10.1007/s11104-007-9233-5 Arshad M, Frankenberger WT (1991) Microbial production of plant hormones. Plant Soil. doi:10.1007/BF00011893 Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013) Application of natural blends of phytochemicals derived from the root exudates of arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288:4502–4512. doi:10.1074/jbc.M112.433300 Balla I, Vértesy J, Köves-Péchy K, Vörös I, Bujtás Z, Bíró B (1998) Acclimation results of micropropagated black locust (Robina pseudoacacia L.) improved by symbiotic micro-organisms. Plant Cell Tissue Organ Cult 52:113–115. doi:10.102 3/A:1005974024515 Barka EA, Belarbi A, Hachet C, Nowak J, Audran J-C (2000) Enhancement of in  vitro growth and resistance to gray mould of Vitis vinifera co-cultured with plant growth-promoting rhizobacteria. FEMS Microbiol Lett. doi:10.1111/j.1574-6968.2000. tb09087.x Barka EA, Gognies S, Nowak J, Audran J, Belarbi A (2002) Inhibitory efect of endophyte bacteria on Botrytis cinerea and its inluence to promote grapevine growth. Biol Control. doi:10.1016/ S1049-9644(02)00034-8 Barka EA, Nowak J, Clément S (2006) Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growthpromoting rhizobacterium, Burkholderia phytoirmans strain PsJN. Appl Env Microbiol. doi:10.1128/AEM.01047-06 Bashan Y (1998) Inoculants of plant growth-promoting bacteria for use in agriculture. Biotechnol Adv 16:729–770. doi:10.1016/ S0734-9750(98)00003-2 Bashan Y, de-Bashan LE, Prabhu SR, Hernandez J-P (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). Plant Soil 378:1–33. doi:10.1007/s11104-013-1956-x Bensalim S, Nowak J, Asiedu SK (1998) A plant growth promoting rhizobacterium and temperature efects on performance of 18 clones of potato. Am J Potato Res. doi:10.1007/BF02895849 Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1. doi:10.1111/j.1574-6941.2009.00654.x Berg G, Grube M, Schloter M, Smalla K (2014) Unraveling the plant microbiome: looking back and future perspectives. Front Microbiol 5:148. doi:10.3389/fmicb.2014.00148 Bergey DH, Krieg NR, Holt JG (1984) Bergey’s manual of systematic bacteriology. Williams & Wilkins, Baltimore Bhawana, Stubbleield JM, Newsome AL, Cahoon AB (2015) Surface decontamination of plant tissue explants with chlorine

Plant Cell Tiss Organ Cult dioxide gas. In Vitro Cell Dev Biol 51:214–219. doi:10.1007/ s11627-014-9659-4 Bordiec S, Paquis S, Lacroix H, Dhondt S, Ait Barka E, Kaufmann S, Jeandet P, Mazeyrat-Gourbeyre F, Clement C, Baillieul F, Dorey S (2011) Comparative analysis of defence responses induced by the endophytic plant growth-promoting rhizobacterium Burkholderia phytoirmans strain PsJN and the nonhost bacterium Pseudomonas syringae pv. pisi in grapevine cell suspensions. J Exp Bot 62:595–603. doi:10.1093/jxb/ erq291 Bottini R, Cassan F, Piccoli P (2004) Gibberellin production by bacteria and its involvement in plant growth promotion and yield increase. Appl Microbiol Biotechnol 65:497–503. doi:10.1007/s00253-004-1696-1 Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37. doi:10.1016/j.copbio.2013.09.012 Buckley PM, DeWilde TN, Reed BM (1995) Characterization and identiication of bacteria isolated from micropropagated mint plants. In  Vitro Cell Dev Biol 31:58–64. doi:10.1007/ BF02632229 Bunn E, Tan B (2002) Microbial contaminants in plant tissue culture propagation. In: Sivasithamparama K, Dixon KW, Barrett RL (eds) Microorganisms in plant conservation and biodiversity. Springe, Dordrecht, pp 307–335 Burlak OP, de Vera J-P, Yatsenko V, Kozyrovska NO (2013) Putative mechanisms of bacterial efects on plant photosystem under stress. Biopolym Cell 29:3–10 Burns JA, Schwarz OJ (1996) Bacterial stimulation of adventitious rooting on in  vitro cultured slash pine (Pinus elliottii Engelm.) seedling explants. Plant Cell Rep 15:405–408. doi:10.1007/BF00232064 Cain CC, Henry AT, Waldo RH, Casida LJ, Falkinham JO (2000) Identiication and characteristics of a novel Burkholderia strain with broad-spectrum antimicrobial activity. Appl Environ Microbiol 66:4139–4141. doi:10.1128/ AEM.66.9.4139-4141.2000 Carletti S, Llorente B, Caceres E, Tandecarz J (1998) Jojoba inoculation with Azospirillum brasilense stimulates in  vitro root formation. Plant Tissue Cult Biotechnol 4:165–174 Carvalho TLG, Ballesteros HGF, Thiebaut F, Ferreira PCG, Hemerly AS (2016) Nice to meet you: genetic, epigenetic and metabolic controls of plant perception of beneicial associative and endophytic diazotrophic bacteria in nonleguminous plants. Plant Mol Biol 90:561–574. doi:10.1007/ s11103-016-0435-1 Cassells AC (1991) Problems in tissue culture: culture contamination. In: Debergh PC, Zimmerman RH (eds) Micropropagation: technology and application. Kluwer Academic Publishers, Dordrecht, pp 31–44 Cassells AC (1997) Pathogen and microbial contamination management in micropropagation—an overview. In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Kluwer Academic Publishers, Dordrecht, pp 1–13 Cassells AC (2011) Detection and elimination of microbial endophytes and prevention of contamination in plant tissue culture. In: Trigiano RN, Gray DJ (eds) Plant tissue culture, development, and biotechnology. CRC Press, Boca Raton, pp 223–238 Cassells AC, Doyle BM (2006) Pathogen and biological contamination management. In: Loyola-Vargas FM, Vazquez-Flota F (eds) Plant methods in molecular biology: plant cell culture protocols, 2nd edn, vol 318. Humana Press Inc., Totowa, pp 35–50 Cassells AC, Tahmatsidou V (1996) The inluence of local plant growth conditions on non-fastidious bacterial contamination of meristem-tips of Hydrangea cultured in vitro. Plant Cell Tissue Organ Cult 47:15–26. doi:10.1007/BF02318961

Chandra S, Bandopadhyay R, Kumar V, Chandra R (2010) Acclimatization of tissue cultured plantlets: from laboratory to land. Biotechnol Lett 32:1199–1205. doi:10.1007/ s10529-010-0290-0 Compant S, Dufy B, Nowak J, Clément C, Barka EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action and future prospects. Appl Env Microbiol. doi:10.1128/AEM.71.9.4951-4959.2005 Compant S, Kaplan H, Sessitsch A, Nowak J, Ait Barka E, Clement C (2008a) Endophytic colonization of Vitis vinifera L. by Burkholderia phytoirmans strain PsJN: from the rhizosphere to inlorescence tissues. FEMS Microbiol Ecol 63:84–93. doi:10.1111/j.1574-6941.2007.00410.x Compant S, Nowak J, Coenye T, Clement C, Ait Barka E (2008b) Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol Rev 32:607. doi:10.1111/j.1574-6976.2008.00113.x Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A (2011) Endophytes of grapevine lowers, berries, and seeds: identiication of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb Ecol 62:188–197. doi:10.1007/s00248-011-9883-y Compant S, Brader G, Muzammil S, Sessitsch A, Lebrihi A, Mathieu F (2013) Use of beneicial bacteria and their secondary metabolites to control grapevine pathogen diseases. Biocontrol 58:435– 455. doi:10.1007/s10526-012-9479-6 Conn KL, Lazarovits G, Nowak J (1997) A gnotobiotic bioassay for studying interactions between potatoes and plant growthpromoting rhizobacteria. Can J Microbiol 43:801–808. doi:10.1139/m97-117 de Almeida CV, Andreote FD, Yara R, Tanaka FAO, Azevedo JL, de Almeida M (2009) Bacteriosomes in axenic plants: endophytes as stable endosymbionts. World J Microbiol Biotechnol 25:1757–1764. doi:10.1007/s11274-009-0073-8 Dias ACF, Costa FEC, Andreote FD, Lacava PT, Teixeira MA, Assumpção LC, Araújo WL, Azevedo JL, Melo IS (2009) Isolation of micropropagated strawberry endophytic bacteria and assessment of their potential for plant growth promotion. World J Microbiol Biotechnol 25:189–195. doi:10.1007/ s11274-008-9878-0 Digat B, Brochard P, Hermelin V, Tozet M (1987) Interest of bacterized synthetic substrates MILCAP® for in  vitro culture. Acta Hortic 212:375–378 Dimkpa C, Weinand T, Asch F (2009) Plant-rhizobacteria interactions alleviate abiotic stress conditions. Plant Cell Environ 32:1682– 1694. doi:10.1111/j.1365-3040.2009.02028.x Dufy EM, Hurley EM, Cassells AC (1999) Weaning performance of potato microplants following bacterization and mycorrhization. Potato Res 42:521–527. doi:10.1007/BF02358168 Dunaeva S, Osledkin Y (2015) Bacterial microorganisms associated with the plant tissue culture: identiication and possible role. Agric Biol 50:3–15 Efremova N, Welters P, Lührs R (2012) Protoplast cultures as a source to determine the spectrum of endophytes. Current aspects of European endophyte research. COST Action FA 1103 Endophytes Biotechnol Agric Workshop vol 11, pp 28–30 Falkiner F (1997) Antibiotics in plant tissue culture and micropropagation—what are we aiming at? In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Kluwer Academic Publishers, Dordrecht, pp 155–160 Fang J-Y, Hsu Y-R (2012) Molecular identiication and antibiotic control of endophytic bacterial contaminants from micropropagated Aglaonema cultures. Plant Cell Tissue Organ Cult 110:53–62. doi:10.1007/s11240-012-0129-6 Faria DC, Dias ACF, Melo IS, de Carvalho Costa FE (2013) Endophytic bacteria isolated from orchid and their potential to

13

Plant Cell Tiss Organ Cult promote plant growth. World J Microbiol Biotechnol 29:217– 221. doi:10.1007/s11274-012-1173-4 Fernandez O, Theocharis A, Bordiec S, Feil R, Jacquens L, Clément C, Fontaine F, Ait Barka E (2012) Burkholderia phytoirmans PsJN acclimates grapevine to cold by modulating carbohydrate metabolism. Mol Plant–Microbe Interact MPMI 25:496–504. doi:10.1094/MPMI-09-11-0245 Fletcher J, Leach JE, Eversole K, Tauxe R (2013) Human pathogens on plants: designing a multidisciplinary strategy for research. Phytopathology 103:306–315. doi:10.1094/ PHYTO-09-12-0236-IA Friesen ML, Porter SS, Stark SC, von Wettberg EJ, Sachs JL, Martinez-Romero E (2011) Microbially mediated plant functional traits. Annu Rev Ecol Evol Syst 42:23–46 Frommel MI, Nowak J, Lazarovits G (1991) Growth enhancement and developmental modiication of in vitro grown potato (Solanum tuberosum spp. tuberosum) as afected by a nonluorescent Pseudomonas sp. Plant Physiol. doi:10.1104/pp.96.3.928 Giron D, Frago E, Glevarec G, Pieterse CMJ, Dicke M (2013) Cytokinins as key regulators in plant–microbe–insect interactions: connecting plant growth and defence. Funct Ecol 27:599–609. doi:10.1111/1365-2435.12042 Goellner K, Conrath U (2008) Priming: it’s all the world to induced disease resistance. In: Collinge DB, Munk L, Cooke BM (eds) Sustainable disease management in a European context. Springer, Dordrecht, pp 233–242 Gonzalez AJ, Larraburu EE, Llorente BE (2015) Azospirillum brasilense increased salt tolerance of jojoba during in vitro rooting. Ind Crops Prod 76:41–48. doi:10.1016/j.indcrop.2015.06.017 González-Olmedo JL, Fundora Z, Molina LA, Abdulnour J, Desjardins Y, Escalona M (2005) New contributions to propagation of pineapple (Ananas comosus L. Merr) in temporary immersion bioreactors. In Vitro Cell Dev Biol 41:87–90. doi:10.1079/ IVP2004603 Gopinath S, Kumaran KS, Sundararaman M (2015) A new initiative in micropropagation: airborne bacterial volatiles modulate organogenesis and antioxidant activity in tobacco (Nicotiana tabacum L.) callus. In  Vitro Cell Dev Biol 51:514–523. doi:10.1007/s11627-015-9717-6 Grover M, Ali SZ, Sandhya V, Rasul A, Venkateswarlu B (2011) Role of microorganisms in adaptation of agriculture crops to abiotic stresses. World J Microbiol Biotechnol 27:1231–1240. doi:10.1007/s11274-010-0572-7 Guglielmetti S, Basilico R, Taverniti V, Arioli S, Piagnani C, Bernacchi A (2013) Luteibacter rhizovicinus MIMR1 promotes root development in barley (Hordeum vulgare L.) under laboratory conditions. World J Microbiol Biotechnol 29:2025–2032. doi:10.1007/s11274-013-1365-6 Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471. doi:10.1016/j.tim.2008.07.008 Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, van Overbeek LS, van Elsas JD (2011) Rice root-associated bacteria: insights into community structures across 10 cultivars. FEMS Microbiol Ecol 77:154. doi:10.1111/j.1574-6941.2011.01092.x Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for deining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320. doi:10.1128/MMBR.00050-14 Herman E (1987) Toward control of micropropagation contamination. Agricell Rep 9:33–35 Herman E (1990) Non-axenic plant tissue culture: possibilities and opportunities. Acta Hortic 280:233–238 Jaizme-Vega M del C, Rodríguez-Romero, A S, Guerra MSP (2004) Potential use of rhizobacteria from the Bacillus genus to

13

stimulate the plant growth of micropropagated bananas. Fruits 59:83–90. doi:10.1051/fruits:2004008 James M, Blagden T, Moncrief I, Burans JP, Schneider K, Fletcher J (2014) Validation of real-time PCR assays for bioforensic detection of model plant pathogens. J Forensic Sci 59:463–469. doi:10.1111/1556-4029.12321 Kaluzna M, Mikicińsk A, Sobiczewski P, Zawadzka M, Zenkteler E, Orlikowska T (2013) Detection, isolation, and preliminary characterization of bacteria contaminating plant tissue cultures. Acta Agrobot 66:81–92 Kalyaeva M, Ivanova E, Doronina N, Zakharchenko NS, Trotsenko YA, Buryanov YI (2003) The efect of aerobic methylotrophic bacteria on in vitro morphogenesis of soft wheat (Triticum aestivum). Russ J Plant Physiol 50:354–359 Kanchiswamy CN, Malnoy M, Mafei ME (2015) Chemical diversity of microbial volatiles and their potential for plant growth and productivity. Front Plant Sci 6:151. doi:10.3389/ fpls.2015.00151 Kim S, Lowman S, Hou G, Nowak J, Flinn B, Mei C (2012) Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytoirmans strain PsJN. Biotechnol Biofuels 5:37. doi:10.1186/1754-6834-5-37 Klocke E, Abel S, Weinzierl K (2012) The “hidden” endophytes in protoplast cultures-a critical thinking about. Current aspects of European endophyte research Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:216. doi:10.3389/fpls.2014.00216 Kohmura H, Yanagawa T, Tanaka M (1999) An eicient micropropagation system using disinfectant incorporated medium and ilm culture vessel for in vitro plant regeneration of asparagus. Acta Hortic 479:373–380 Kurepin LV, Park JM, Lazarovits G, Bernards MA (2015) Burkholderia phytoirmans-induced shoot and root growth promotion is associated with endogenous changes in plant growth hormone levels. Plant Growth Regul 75:199–207. doi:10.1007/ s10725-014-9944-6 Langens-Gerrits M, Albers M, De Klerk G-J (1997) Hot-water treatment before tissue culture reduces initial contamination in Lilium and Acer. In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Springer, Dordrecht, pp 219–224 Lara-Chavez A, Lowman S, Kim S, Tang Y, Zhang J, Udvardi M, Nowak J, Flinn B, Mei C (2015) Global gene expression proiling of two switchgrass cultivars following inoculation with Burkholderia phytoirmans strain PsJN. J Exp Bot 66:4337–4350. doi:10.1093/jxb/erv096 Larraburu EE, Llorente BE (2015) Azospirillum brasilense enhances in  vitro rhizogenesis of Handroanthus impetiginosus (pink lapacho) in diferent culture media. Ann For Sci 72:219–229. doi:10.1007/s13595-014-0418-9 Larraburu EE, Carletti SM, Cáceres EAR, Llorente BE (2007) Micropropagation of photinia employing rhizobacteria to promote root development. Plant Cell Rep 26:711–717 Larraburu EE, Apóstolo NM, Llorente BE (2010) Anatomy and morphology of photinia (Photinia × fraseri Dress) in  vitro plants inoculated with rhizobacteria. Trees 24:635–642. doi:10.1007/ s00468-010-0433-x Lata H, Li XC, Silva B, Moraes RM, Halda-Alija L (2006) Identiication of IAA-producing endophytic bacteria from micropropagated Echinacea plants using 16 S rRNA sequencing. Plant Cell Tissue Organ Cult 85:353–359. doi:10.1007/ s11240-006-9087-1 Leifert C, Morris CE, Waites WM (1994) Ecology of microbial saprophytes and pathogens in tissue culture and ield-grown plants:

Plant Cell Tiss Organ Cult reasons for contamination problems in vitro. Crit Rev Plant Sci 13:139–183 Lowman JS, Lava-Chavez A, Kim-Dura S, Flinn B, Nowak J, Mei C (2015) Switchgrass ield performance on twosSoils as afected by bacterization of seedlings with Burkholderia phytoirmans Strain PsJN. BioEnergy Res 8:440–449. doi:10.1007/ s12155-014-9536-3 Lucero ME, Unc A, Cooke P, Dowd S, Sun S (2011) Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griithsii. PLoS ONE 6:e17693. doi:10.1371/journal.pone.0017693 Ludwig-Müller J (2015a) Plants and endophytes: equal partners in secondary metabolite production? Biotechnol Lett 37:1325– 1334. doi:10.1007/s10529-015-1814-4 Ludwig-Müller J (2015b) Bacteria and fungi controlling plant growth by manipulating auxin: balance between development and defense. J Plant Physiol 172:4–12. doi:10.1016/j. jplph.2014.01.002 Ma Y, Rajkumar M, Luo Y, Freitas H (2011) Inoculation of endophytic bacteria on host and non-host plants—efects on plant growth and Ni uptake. J Hazard Mater 195:230–237. doi:10.1016/j.jhazmat.2011.08.034 Madmony A, Chernin L, Pleban S, Peleg E, Riov J (2005) Enterobacter cloacae, an obligatory endophyte of pollen grains of Mediterranean pines. Folia Microbiol (Praha) 50:209–216 Marino G, Altan AD, Biavati B (1996) The efect of bacterial contamination on the growth and gas evolution of in vitro cultured apricot shoots. In  Vitro Cell Dev Biol 32:51–56. doi:10.1007/ BF02823014 Marino G, Gaggìa F, Bafoni L, Toniolo C, Nicoletti M (2015) Antimicrobial activity of Melia azedarach fruit extracts for control of bacteria in inoculated in-vitro shoots of “MRS 2/5” plum hybrid and calla lily and extract inluence on the shoot cultures. Eur J Plant Pathol 141:505–521. doi:10.1007/ s10658-014-0559-6 Meldau DG, Long HH, Baldwin IT (2012) A native plant growth promoting bacterium, Bacillus sp. B55, rescues growth performance of an ethylene-insensitive plant genotype in nature. Front Plant Sci 3:112. doi:10.3389/fpls.2012.00112 Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332:1097–1100. doi:10.1126/science.1203980 Mirza MS, Ahmad W, Latif F, Haurat J, Bally R, Normand P, Malik KA (2001) Isolation, partial characterization, and the efect of plant growth-promoting bacteria (PGPB) on micro-propagated sugarcane in  vitro. Plant Soil 237:47–54. doi:10.102 3/A:1013388619231 Mitter B, Petric A, Shin MW, Chain PSG, Hauberg-Lotte L, Reinhold-Hurek B, Nowak J, Sessitsch A (2013) Comparative genome analysis of Burkholderia phytoirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci 4:120. doi:10.3389/ fpls.2013.00120 Miyazaki J, Tan BH, Errington SG (2010) Eradication of endophytic bacteria via treatment for axillary buds of Petunia hybrida using Plant Preservative Mixture (PPMTM). Plant Cell Tissue Organ Cult 102:365–372. doi:10.1007/s11240-010-9741-5 Montañez A, Blanco AR, Barlocco C, Beracochea M, Sicardi M (2012) Characterization of cultivable putative endophytic plant growth promoting bacteria associated with maize cultivars (Zea mays L.) and their inoculation efects in  vitro. Appl Soil Ecol 58:21–28. doi:10.1016/j.apsoil.2012.02.009 Muganu M, Paolocci M, Bignami C, Di Mattia E (2015) Enhancement of adventitious root diferentiation and growth of in vitro

grapevine shoots inoculated with plant growth promoting rhizobacteria. VITIS-J Grapevine Res 54:73–77 Müller P, Döring M (2009) Isothermal DNA ampliication facilitates the identiication of a broad spectrum of bacteria, fungi and protozoa in Eleutherococcus sp. plant tissue cultures. Plant Cell Tissue Organ Cult 98:35–45. doi:10.1007/s11240-009-9536-8 Murthy BNS, Vettakkorumakankav NN, KrishnaRaj S, Odumeru J, Saxena PK (1999) Characterization of somatic embryogenesis in Pelargonium × hortorum mediated by a bacterium. Plant Cell Rep 18:607–613. doi:10.1007/s002990050630 Naveed M, Hussain MB, Zahir ZA, Mitter B, Sessitsch A (2014a) Drought stress amelioration in wheat through inoculation with Burkholderia phytoirmans strain PsJN. Plant Growth Regul 73:121–131. doi:10.1007/s10725-013-9874-8 Naveed M, Mitter B, Reichenauer TG, Wieczorek K, Sessitsch A (2014b) Increased drought stress resilience of maize through endophytic colonization by Burkholderia phytoirmans PsJN and Enterobacter sp. FD17. Environ Exp Bot 97:30–39. doi:10.1016/j.envexpbot.2013.09.014 Naveed M, Mitter B, Yousaf S, Pastar M, Afzal M, Sessitsch A (2014c) The endophyte Enterobacter sp. FD17: a maize growth enhancer selected based on rigorous testing of plant beneicial traits and colonization characteristics. Biol Fertil Soils 50:249– 262. doi:10.1007/s00374-013-0854-y Norman DJ, Alvarez AM (1994) Latent infections of in  vitro anthurium caused by Xanthomonas campestris pv. diefenbachiae. Plant Cell Tissue Organ Cult 39:55–61. doi:10.1007/ BF00037592 Nowak J (1998) Beneits of in vitro “biotization” of plant tissue cultures with microbial inoculants. In Vitro Cell Dev Biol 34:122– 130. doi:10.1007/BF02822776 Nowak J, Shulaev V (2003) Priming for transplant stress resistance in in  vitro propagation. In  Vitro Cell Dev Biol 39:107–124. doi:10.1079/IVP2002403 Nowak J, Bensalim S, Smith CD, Dunbar C, Asiedu SK, Madani A, Lazarovits G, Northcott D, Sturz AV (1999) Behaviour of plant material issued from in  vitro tuberization. Potato Res 42:505– 519. doi:10.1007/BF02358167 Oldroyd GED (2013) Speak, friend, and enter: signalling systems that promote beneicial symbiotic associations in plants. Nat Rev Micro 11:252–263. doi:10.1038/nrmicro2990 Orlikowska T, Zawadzka M, Zenkteler E, Sobiczewski P (2012) Inluence of the biocides PPMtm and Vitrofural on bacteria isolated from contaminated plant tissue cultures and on plant microshoots grown on various media. J Hortic Sci Biotechnol 87:223–230 Orlikowska T, Nowak J, Ogórek L (2017) Burkholderia phytoirmans PsJN promotes in  vitro rooting and acclimatization of Helleborus. Acta Hortic (in press) Owen D, Williams AP, Griith GW, Withers PJA (2015) Use of commercial bio-inoculants to increase agricultural production through improved phosphorous acquisition. Appl Soil Ecol 86:41–54. doi:10.1016/j.apsoil.2014.09.012 Păcurar DI, Thordal-Christensen H, Păcurar ML, Pamil D, Botez C, Bellini C (2011) Agrobacterium tumefaciens: From crown gall tumors to genetic transformation. Physiol Mol Plant Pathol 76:76–81. doi:10.1016/j.pmpp.2011.06.004 Pandey A, Palni LMS, Bag N (2000) Biological hardening of tissue culture raised tea plants through rhizosphere bacteria. Biotechnol Lett 22:1087–1091. doi:10.1023/A:1005674803237 Panicker B, Thomas P, Janakiram T, Venugopalan R, Narayanappa SB (2007) Inluence of cytokinin levels on in vitro propagation of shy suckering chrysanthemum Arka Swarna and activation of endophytic bacteria. In Vitro Cell Dev Biol 43:614–622 Panigrahi S, Aruna Lakshmi K, Venkateshwarulu Y, Umesh N (2015) Biohardening of micropropagated plants with PGPR and

13

Plant Cell Tiss Organ Cult endophytic bacteria enhances the protein content. In: Biotechnology and bioforensics, forensic and medical bioinformatics. pp 51–55 Park JM, Lazarovits G (2014) Involvement of hexokinase1 in plant growth promotion as mediated by Burkholderia phytoirmans. Can J Microbiol 60:343–354. doi:10.1139/cjm-2014-0053 Parray JA, Kamili AN, Reshi ZA, Quadri RA, Jan S (2015) Interaction of rhizobacterial strains for growth improvement of Crocus sativus L. under tissue culture conditions. Plant Cell Tissue Organ Cult (PCTOC) 121:325–334. doi:10.1007/s11240-014-0703-1 Partida-Martinez LP, Heil M (2011) The microbe-free plant: fact or artifact? Front Plant Sci 2:100. doi:10.3389/fpls.2011.00100 Patten CL, Glick BR (2002) Role of Pseudomonas putida indoleacetic acid in development of the host plant root system. Appl Environ Microbiol 68:3795–3801. doi:10.1128/ AEM.68.8.3795-3801.2002 Pillay VK, Nowak J (1997) Inoculum density, temperature, and genotype efects on in  vitro growth promotion and epiphytic and endophytic colonization of tomato (Lycopersicon esculentum L.) seedlings inoculated with a pseudomonad bacterium. Can J Microbiol 43:354–361. doi:10.1139/m97-049 Pirttilä AM, Laukkanen H, Pospiech H, Myllylä R, Hohtola A (2000) Detection of intracellular bacteria in the buds of Scotch Pine (Pinus sylvestris L.) by in  situ hybridization. Appl Environ Microbiol 66:3073–3077 Pirttilä AM, Podolich O, Koskimäki JJ, Hohtola E, Hohtola A (2008) Role of origin and endophyte infection in browning of budderived tissue cultures of Scots pine (Pinus sylvestris L.). Plant Cell Tissue Organ Cult 95:47–55 Pischke MS, Huttlin EL, Hegeman AD, Sussman MR (2006) A transcriptome-based characterization of habituation in plant tissue culture. Plant Physiol 140:1255–1278 Podolich O, Laschevskyy V, Ovcharenko L, Kozyrovska N, Pirttilä AM (2009) Methylobacterium sp. resides in unculturable state in potato tissues in  vitro and becomes culturable after induction by Pseudomonas luorescens IMGB163. J Appl Microbiol 106:728–737. doi:10.1111/j.1365-2672.2008.03951.x Pohjanen J, Koskimaki J, Pirttilä A (2014) Interaction of meristemassociated endophytic bacteria. In: Verma YC, Gange AC (eds) Advances in endophytic research. Springer, New Delhi, pp 103–113 Poppenberger B, Leonhardt W, Redl H (2002) Latent persistence of Agrobacterium vitis in micropropagated Vitis vinifera. VITIS-J Grapevine Res 41:113–114 Poupin MJ, Timmermann T, Vega A, Zuñiga A, González B (2013) Efects of the plant growth-promoting bacterium Burkholderia phytoirmans PsJN throughout the life cycle of Arabidopsis thaliana. PLoS ONE 8:e69435. doi:10.1371/journal. pone.0069435 Quambusch M, Pirttilä AM, Tejesvi MV, Winkelmann T, Bartsch M (2014) Endophytic bacteria in plant tissue culture: diferences between easy- and diicult-to-propagate Prunus avium genotypes. Tree Physiol 34:524–533. doi:10.1093/treephys/tpu027 Rakotoniriana EF, Rafamantanana M, Randriamampionona D, Rabemanantsoa C, Urveg-Ratsimamanga S, El Jaziri M, Munaut F, Corbisier A-M, Quetin-Leclercq J, Declerck S (2013) Study in vitro of the impact of endophytic bacteria isolated from Centella asiatica on the disease incidence caused by the hemibiotrophic fungus Colletotrichum higginsianum. Antonie Van Leeuwenhoek 103:121–133 Rames E, Hamili E, Kurtböke I (2009) Bacterially-induced growth promotion of micropropagated ginger. Acta Hortic 829:155–159 Reed BM, Tanprasert P (1995) Detection and control of bacterial contaminants of plant tissue cultures. A review of recent literature. Plant Tissue Cult Biotechnol 1:137–142

13

Reed BM, Buckley PM, DeWilde TN (1995) Detection and eradication of endophytic bacteria from micropropagated mint plants. In Vitro Cell Dev Biol-Plant 31:53–57 Reed BM, Mentzer J, Tanprasert P, Yu X (1997) Internal bacterial contamination of micropropagated hazelnut: identiication and antibiotic treatment. In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Kluwer Academic Publishers, Dordrecht, pp 233–236 Rolli E, Marasco R, Vigani G, Ettoumi B, Mapelli F, Deangelis ML, Gandoli C, Casati E, Previtali F, Gerbino R, Pierotti Cei F, Borin S, Sorlini C, Zocchi G, Dafonchio D (2015) Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environ Microbiol 17:316–331. doi:10.1111/1462-2920.12439 Rosenberg E, Sharon G, Atad I, Zilber-Rosenberg I (2010) The evolution of animals and plants via symbiosis with microorganisms. Environ Microbiol Rep 2:500–506. doi:10.1111/j.1758-2229.2010.00177.x Rosenblueth M, Martinez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant–Microbe Interact MPMI 19:827–837. doi:10.1094/MPMI-19-0827 Rout ME, Chrzanowski TH, Westlie TK, DeLuca TH, Callaway RM, Holben WE (2013) Bacterial endophytes enhance competition by invasive plants. Am J Bot 100:1726–1737. doi:10.3732/ ajb.1200577 Rowntree JK (2006) Development of novel methods for the initiation of in vitro bryophyte cultures for conservation. Plant Cell Tissue Organ Cult 87:191–201. doi:10.1007/s11240-006-9154-7 Ruiz S, Adriano L, Ovando I, Navarro C, Salvador M (2011) Biofertilization of micropropagated Agave tequilana: Efect on plant growth and production of hydrolytic enzymes. Afr J Biotechnol 10:9631–9646 Russo A, Vettori L, Felici C, Fiaschi G, Morini S, Tofanin A (2008) Enhanced micropropagation response and biocontrol efect of Azospirillum brasilense Sp245 on Prunus cerasifera L. clone Mr.S  2/5 plants. J Biotechnol 134:312–319. doi:10.1016/j. jbiotec.2008.01.020 Saleem M, Arshad M, Hussain S, Bhatti AS (2007) Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. J Ind Microbiol Biotechnol 34:635–648. doi:10.1007/s10295-007-0240-6 Salomon MV, Bottini R, de Souza Filho GA, Cohen AC, Moreno D, Gil M, Piccoli P (2014) Bacteria isolated from roots and rhizosphere of Vitis vinifera retard water losses, induce abscisic acid accumulation and synthesis of defense-related terpenes in in  vitro cultured grapevine. Physiol Plant 151:359–374. doi:10.1111/ppl.12117 Santhanam R, Baldwin IT, Groten K (2015) In wild tobacco, Nicotiana attenuata, variation among bacterial communities of isogenic plants is mainly shaped by the local soil microbiota independently of the plants’ capacity to produce jasmonic acid. Commun Integr Biol 8:e1017160. doi:10.1080/19420889.2015. 1017160 Santoro MV, Cappellari LR, Giordano W, Banchio E (2015) Plant growth-promoting efects of native Pseudomonas strains on Mentha piperita (peppermint): an in  vitro study. Plant Biol 17:1218–1226. doi:10.1111/plb.12351 Saravanakumar D (2012) Rhizobacterial ACC deaminase in plant growth and stress amelioration. In: Maheshwari DK (ed) Bacteria in agrobiology: stress management. Springer, Berlin, pp. 187–210 Sawana A, Adeolu M, Gupta RS (2014) Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the amended genus Burkholderia containing pathogenic organisms and a new genus

Plant Cell Tiss Organ Cult Paraburkholderia gen. nov. harboring environmental species. Front Genet 5:429. doi:10.3389/fgene.2014.00429 Scherling C, Ulrich K, Ewald D, Weckwerth W (2009) A metabolic signature of the beneicial interaction of the endophyte Paenibacillus sp. isolate and in vitro-grown poplar plants revealed by metabolomics. Mol Plant–Microbe Interact MPMI 22:1032– 1037. doi:10.1094/MPMI-22-8-1032 Segers P, Vancanneyt M, Pot B, Torck U, Hoste B, Dewettinck D, Falsen E, Kersters K, De Vos P (1994) Classiication of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Busing, Döll, and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov, respectively. Int J Syst Bacteriol 44:499–510. doi:10.1099/00207713-44-3-499 Senthilkumar M, Madhaiyan M, Sundaram SP, Sangeetha H, Kannaiyan S (2008) Induction of endophytic colonization in rice (Oryza sativa L.) tissue culture plants by Azorhizobium caulinodans. Biotechnol Lett 30:1477–1487. doi:10.1007/ s10529-008-9693-6 Senthilkumar M, Anandham R, Madhaiyan M, Venkateshwarulu V, Sa T (2011) Endophytic bacteria: perspectives and applications in agricultural crop production. In: Maheshwari DK (ed) Bacteria in agrobiology:crop ecosystems. Springer, Berlin, Heidelberg, pp 61–96 Sessitsch A, Coenye T, Sturz AV, Vandamme P, Barka EA, Salles JF, Elsas JD, Faure D, Reiter B, Glick BR, Wang-Pruski G, Nowak J (2005) Burkholderia phytoirmans sp. nov., a novel plantassociated bacterium with plant-beneicial properties. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.63149-0 Sessitsch A, Hardoim P, Doring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T, Sarkar A, Bodrossy L, van Overbeek L, Brar D, van Elsas JD, Reinhold-Hurek B (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant–Microbe Interact MPMI 25:28–36. doi:10.1094/MPMI-08-11-0204 Sharma VK, Nowak J (1998) Enhancement of verticillium wilt resistance in tomato transplants by in  vitro co-culture of seedlings with a plant growth promoting rhizobacterium (Pseudomonas sp. strain PsJN). Can J Microbiol 44:528–536. doi:10.1139/ w98-017 Shetty K, Curtis OF, Levin RE, Witkowsky R, Ang W (1995) Prevention of vitriication associated with in  vitro shoot culture of oregano (Origanum vulgare) by Pseudomonas spp. J Plant Physiol 147:447–451. doi:10.1016/S0176-1617(11)82181-4 Spaepen S, Vanderleyden J, Remans R (2007) Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 31:425–448 Stead D, Elphinstone J, Weller S, Smith N, Hennesy J (2000) Modern methods for characterizing, identifying and detecting bacteria associated with plants. Acta Hortic 530:45–55 Su F, Jacquard C, Villaume S, Michel J, Rabenoelina F, Clement C, Barka EA, Dhondt-Cordelier S, Vaillant-Gaveau N (2015) Burkholderia phytoirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana. Front Plant Sci 6:810. doi:10.3389/fpls.2015.00810 Su F, Gilard F, Guérard F, Citerne S, Clément C, Vaillant-Gaveau N, Dhondt-Cordelier S (2016) Spatio-temporal responses of arabidopsis leaves in photosynthetic performance and metabolite contents to Burkholderia phytoirmans PsJN. Front Plant Sci 7:403. doi:10.3389/fpls.2016.00403 Suada EP, Jasim B, Jimtha CJ, Gayatri GP, Radhakrishnan EK, Remakanthan A (2015) Phytostimulatory and hardening periodreducing efects of plant-associated bacteria on micropropagated Musa acuminata cv. Grand Naine. In Vitro Cell Dev Biol 51:682–687. doi:10.1007/s11627-015-9721-x

Suarez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonca-Previato L, James EK, Venturi V (2012) Common features of environmental and potentially beneicial plant-associated Burkholderia. Microb Ecol 63:249–266. doi:10.1007/ s00248-011-9929-1 Sunayana MR, Sasikala C, Ramana CV (2005) Rhodestrin: A novel indole terpenoid phytohormone from Rhodobacter sphaeroides. Biotechnol Lett 27:1897–1900. doi:10.1007/ s10529-005-3900-5 Szendrák E, Read P, Yang G (1997) Prevention and elimination of contamination for in  vitro culture of several woody species. In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Kluwer Academic Publishers, Dordrecht, pp 233–236 Theocharis A, Bordiec S, Fernandez O, Paquis S, Dhondt-Cordelier S, Baillieul F, Clement C, Barka EA (2012) Burkholderia phytoirmans PsJN primes Vitis vinifera L. and confers a better tolerance to low nonfreezing temperatures. Mol Plant–Microbe Interact MPMI 25:241–249. doi:10.1094/ MPMI-05-11-0124 Thomas P (2004a) A three-step screening procedure for detection of covert and endophytic bacteria in plant tissue cultures. Curr Sci (Banglore) 87:67–72 Thomas P (2004b) Isolation of Bacillus pumilus from in  vitro grapes as a long-term alcohol-surviving and rhizogenesis inducing covert endophyte. J Appl Microbiol 97:114–123. doi:10.1111/j.1365-2672.2004.02279.x Thomas P (2011) Intense association of non-culturable endophytic bacteria with antibiotic-cleansed in vitro watermelon and their activation in degenerating cultures. Plant Cell Rep 30:2313– 2325. doi:10.1007/s00299-011-1158-z Thomas P, Sekhar AC (2014) Live cell imaging reveals extensive intracellular cytoplasmic colonization of banana by normally non-cultivable endophytic bacteria. AoB Plants. doi:10.1093/ aobpla/plu002 Thomas P, Prabhakara BS, Pitchaimuthu M (2006) Cleansing the long-term micropropagated triploid watermelon cultures from covert bacteria and ield testing the plants for clonal idelity and fertility during the 7–10 year period in vitro. Plant Cell Tissue Organ Cult 85:317–329. doi:10.1007/s11240-006-9083-5 Thomas P, Kumari S, Swarna GK, Gowda TKS (2007) Papaya shoot tip associated endophytic bacteria isolated from in  vitro cultures and host-endophyte interaction in vitro and in vivo. Can J Microbiol 53:380–390. doi:10.1139/W06-141 Thomas J, Ajay D, Raj Kumar R, Mandal AKA (2010) Inluence of beneicial microorganisms during in  vivo acclimatization of in vitro-derived tea (Camellia sinensis) plants. Plant Cell Tissue Organ Cult 101:365–370. doi:10.1007/s11240-010-9687-7 Trivedi P, Pandey A (2007) Biological hardening of micropropagated Picrorhiza kurrooa Royel ex Benth., an endangered species of medical importance. World J Microbiol Biotechnol 23:877– 878. doi:10.1007/s11274-006-9293-3 Tsao C-W, Postman JD, Reed BM (2000) Virus infections reduce in  vitro multiplication of “Malling Landmark” raspberry. In Vitro Cell Dev Biol Plant 36:65–68 Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209. doi:10.1186/gb-2013-14-6-209 Ueno K, Shetty K (1997) Efect of selected polysaccharide-producing soil bacteria on hyperhydricity control in oregano tissue cultures. Appl Environ Microbiol 63:767–770 Ueno K, Cheplick S, Shetty K (1998) Reduced hyperhydricity and enhanced growth of tissue culture-generated raspberry (Rubus sp.) clonal lines by Pseudomonas sp. isolated from oregano. Process Biochem 33:441–445 Ulrich K, Stauber T, Ewald D (2008) Paenibacillus—a predominant endophytic bacterium colonising tissue cultures of woody

13

Plant Cell Tiss Organ Cult plants. Plant Cell Tissue Organ Cult 93:347–351. doi:10.1007/ s11240-008-9367-z Vacheron J, Desbrosses G, Boufaud M-L, Touraine B, MoenneLoccoz Y, Muller D, Legendre L, Wisniewski-Dye F, PrigentCombaret C (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4:356. doi:10.3389/ fpls.2013.00356 Vereecke D, Burssens S, Simón-Mateo C, Inzé D, Van Montagu M, Goethals K, Jaziri M (2000) The Rhodococcus fascians-plant interaction: morphological traits and biotechnological applications. Planta 210:241–251. doi:10.1007/PL00008131 Vestberg M, Cassells A (2009) The use of AMF and PGPR inoculants singly and combined to promote microplant establishment, growth and health. In: Varma A, Kharkwal AC (eds) Fungi symbiotic, biology soil. Springer, Berlin, pp 337–360 Vettori L, Russo A, Felici C, Fiaschi G, Morini S, Tofanin A (2010) Improving micropropagation: efect of Azospirillum brasilense Sp245 on acclimatization of rootstocks of fruit tree. J Plant Interact 5:249–259. doi:10.1080/17429145.2010.511280 Wang B, Mei C, Seiler JR (2015) Early growth promotion and leaf level physiology changes in Burkholderia phytoirmans strain PsJN inoculated switchgrass. Plant Physiol Biochem PPB 86:16–23. doi:10.1016/j.plaphy.2014.11.008 Weilharter A, Mitter B, Shin MV, Chain PSG, Nowak J, Sessitsch A (2011) Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytoirmans strain PsJN. J Bacteriol 193:3383–3384. doi:10.1128/JB.05055-11 Wilson D (1995) Endophyte: The evolution of a term, and clariication of its use and deinition. Oikos 73:274–276. doi:10.2307/3545919 Xie X, Zhang H, Pare PW (2009) Sustained growth promotion in arabidopsis with long-term exposure to the beneicial soil bacterium Bacillus subtilis (GB03). Plant Signal Behav 4:948–953 Yang Y-S, Wada K, Goto M, Futsuhara Y (1991) In vitro formation of nodular calli in soybean (Glycine max L.) induced by cocultivated Pseudomonas maltophilia. Jpn J Breed 41:595–604 Young L-S, Hameed A, Peng S-Y, Shan Y-H, Wu S-P (2013) Endophytic establishment of the soil isolate Burkholderia sp.

13

CC-Al74 enhances growth and P-utilization rate in maize (Zea mays L.). Appl Soil Ecol 66:40–47. doi:10.1016/j. apsoil.2013.02.001 Zakharchenko NS, Kochetkov VV, Buryanov YI, Boronin AM (2011) Efect of rhizosphere bacteria Pseudomonas aureofaciens on the resistance of micropropagated plants to phytopathogens. Appl Biochem Microbiol 47:661. doi:10.1134/S0003683811070118 Zamioudis C, Mastranesti P, Dhonukshe P, Blilou I, Pieterse CMJ (2013) Unraveling root developmental programs initiated by beneicial Pseudomonas spp. bacteria. Plant Physiol 162:304– 318. doi:10.1104/pp.112.212597 Zawadzka M, Trzciński P, Nowak K, Orlikowska T (2014) The impact of three bacteria isolated from contaminated plant cultures on in vitro multiplication and rooting of microshoots of four ornamental plants. J Hortic Res 21:41. doi:10.2478/johr-2013-0020 Zenkteler E, Wlodarczak K, Klosowska M (1997) The application of antibiotic and sulphonamide for eliminating Bacillus cereus during the micropropagation of infected Diefenbachia picta Schott. In: Cassells AC (ed) Pathogen and microbial contamination management in micropropagation. Kluwer Academic Publishers, Dordrecht, pp 233–236 Zhao S, Wei H, Lin C-Y, Zeng Y, Tucker MP, Himmel ME, Ding S-Y (2016) Burkholderia phytoirmans inoculation-induced changes on the shoot cell anatomy and iron accumulation reveal novel components of arabidopsis-endophyte Interaction that can beneit downstream biomass deconstruction. Front Plant Sci 7:24. doi:10.3389/fpls.2016.00024 Ziemienowicz A (2014) Agrobacterium-mediated plant transformation: factors, applications and recent advances. Biocatal Agric Biotechnol 3:95–102. doi:10.1016/j.bcab.2013.10.004 Zúñiga A, Poupin MJ, Donoso R, Ledger T, Guiliani N, Gutierrez RA, Gonzalez B (2013) Quorum sensing and indole-3-acetic acid degradation play a role in colonization and plant growth promotion of Arabidopsis thaliana by Burkholderia phytoirmans PsJN. Mol Plant–Microbe Interact MPMI 26:546–553. doi:10.1094/MPMI-10-12-0241-R