Very nice question. Yes , there is a strong possibility of plant endophytic microbes to be isolated and studies for plants responsiveness.

Thank you for sharing the question with me, Anoop Kumar.

Unfortunately I can not offer a valid response because your question is about a topic that is not my field of expertise.

Maybe next time.

Regards.

For the growth and development of any plant, N & P are limiting factors. Based on plant-microbe interaction we found the following hypothesis mentioned below-

In pulses: SYM-pathway is complete due to presence of different kinds of rhizobia and AM fungi which supply nitrogen (N-fixation) and phosphorus (P- solubilization/mobilization), respectively to the plant in return microbes get nutrient from plant (C-source)

In cereals: SYM pathway is incomplete due to absence of rhizobia but presence of AM fungi, however, the presence of endophyte as nitrogen fixer are there inside the tissue. If we explore them using right kind of strategy then it is feasible that we will get success to make the complete SYM pathway by genetic manipulation of endophytes.

In oilseed: Rudimentary SYM pathway due to lack of BOTH, hence, we have to have only one alternative i.e. endophytes which makes the SYM pathway complete.

Overall, if we progress based on these hypothesis then we will certainly make- nitrogen fixing cereal and oilseeds as well as P-fixing or mobilizes plant in future and this is only possible if we explore the right kind of endophytes.

So far, many reports are available endophytes as PGPR, but yet there is no reports which said that endophytes are better than soil microbes.

However, soil microbes are directly exposed to different kind of environment which is not there in case of endophytes. Therefore in my opinion, if we harness more endophyte than soil microbes, then this may provide better crop responsiveness.

Dear Dr. Anoop Kumar Srivastava,

Since endophytic bacteria live within the plant, they could be better protected from biotic and abiotic stresses in comparison to rhizospheric bacteria. As endophytic PGPRs colonize an ecological niche similar to certain plant pathogens, they are likely candidates for biocontrol agents. There is a good paper (following link) about endophytic bacteria may be useful for you.

Best regards,

http://www.sciencedirect.com/science/article/pii/S0038071709004398

Piriformospora

Piriformospora

Scientific classification

Kingdom:

Fungi

Division:

Basidiomycota

Class:

Agaricomycetes

Order:

Sebacinales

Family:

Sebacinaceae

Genus:

Piriformospora

Species:Piriformospora indica

Type species Piriformospora indica

Sav.Verma, Aj.Varma, Rexer, G.Kost & P.Franken (1998)

Piriformospora is a fungal genus of the order Sebacinales. It is a monotypic genus, containing the single endophytic root-colonising speciesPiriformospora indica, discovered from orchid plants in the Thar desert in Rajasthan, India by Prof. Ajit Verma and group, School of Life Sciences, Jawaharlal Nehru University, New Delhi. The fungus has typical pear-shaped chlamydospores, and thus, named as P. indica .

Unlikemycorrhizal fungi, which cannot be cultured axenically, P. indica can be easily grown on various substrates. It has been found to promote plant growth during its mutualistic symbiotic relationship with a wide variety of plants.[1] Experiments have shown that P. indica increases theresistance of colonized plants against fungal pathogens.[2] It has also been found in experiments with barley that P. indica-inoculated plants are tolerant to salt stress and more resistant to root pathogens. P. indica-infested roots also show antioxidant capacity. The fungus also induces systemic disease resistance in plants.[3] P. indica was found to require host cell death for proliferation during mutualistic symbiosis in barley.[4]Its genome has been sequenced and was published in 2011.[5]

External links[edit]

List of publications on P. indica*[1]

References[edit]

Jump up^ Verma S, Varma A, Rexer K-H, Hassel A, Kost G, Sarbhoy A, Bisen P, Bütehorn B, Franken P. (1998). "Piriformospora indica, gen. et sp. nov., a new root-colonizing fungus". Mycologia 90 (5): 896–903. doi:10.2307/3761331.

Jump up^ Serfling A, Wirsel SG, Lind V, Deising HB. (2007). "Performance of the biocontrol fungus Piriformospora indica on wheat under greenhouse and field conditions". Phytopathology 97 (4): 523–31.doi:10.1094/PHYTO-97-4-0523. PMID 18943293.

Jump up^ Waller F, Achatz B, Baltruschat H, Fodor J, Becker K, Fischer M, Heier T, Hückelhoven R, Neumann C, von Wettstein D, Franken P, Kogel KH. (2005). "The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield". Proceedings of the National Academy of Sciences USA 102 (38): 13386–91.doi:10.1073/pnas.0504423102. PMC 1224632. PMID 16174735.

Dear Colleagues, The role of endophytic symbionts is developing rapidly.

I am including this to show how this can be related to better ability to flourish in extreme environments. 

This organism unlike the majority of mycorrhizal fungi is cultural in vitro making its study and development somewhat easier. It also has ability to produce resistance spore types favoring its commercialization distribution and shelf life. This is just a tip of a very huge ice berg of scientific and technological potential. 

Interesting how many of Indian issues can be addressed in the Indian desert. 

Interesting responses indeed . Unfortunately the earlier responses from Dr Hepperly are not displayed here , the discussion would  have been more interesting . He raised some very important issues.

The plant endophytic microbes , especially bacteria ( the most studied  microbial community ) , they form different kinds of associations with with palnt internal tissues like , symbiotic , mutualistic , commensalistic and trophobiotic  while describing the plant -microbiome interaction . What is the epicenter of such interaction ?. Is it predominantly rhizosphere or somewhere else?. Such endophytic microbes hold great potential for phytoremediation as well . Your comments friends.  

What are the target tissues we should look at while isolating such endophytic microbes. Do you feel microbes from rhizosphere have any similarity to that of plant tissues.

Nice issues you have raised Dr Deka. Efforts have been made to isolate the microbes from rhizosphere as usual , rhizoplanes, phylloplanes, fruit planes, and not sure about different tissues  like root tissues , leaf tissues, bark tissues, xylem sieves, phloem issues, flowers , different parts of fruits ... but all inconclusively . If any one can add something additional , I will highly appreciate.

I am enclosing one excellent PDF by Dr Robert P. Ryan about the endophyte bacteria:  Recent developments and applications , worth reading friends.

Thank you very much prof for giving me a chance to see questions and answers from professors like you around the globe. I am a student and I am learning a lot from these.

Thanks again

Thanks Hussain for appreciating .Hope it proves to be mutual , you are always a learner  in research .

Let me add another very interesting facts about the plant -derived endophytic microorganisms. Such microbes are considered as growth promoting microorganisms something like rhizobacteria. Plant growth promoting endophytes can  promote plant growth by a number of processes similar to rhizobacteria like phosphate solubilization , indole acetic acid production and production of siderophores. , besides secretion of vitamins inside the host plants . Endophytic microorganisms also provide the host plants , the desired preparedness for osmotic adjustments , stomatal regulation , modification of root morphology , elevated nutrient uptake , and alteration in N-metabolism  . Such microbes are also being used in forest regeneration and phytoremediation of contaminated soils. It is  also claimed  for systemic induced resistance  , phenotypically similar to systemic acquired resistance . So use of plant endophytic microbes are gradually catching the eyes of researchers worldover.

If we consider rhizobacteria synonymous to plant endophytic bacteria, how should we inoculate them in plant or we should inoculate in rhizosphere.

Endo is a greek word meaning inside. Endophytes literally means inside the plant tissues but not necessarily inside the cell wall per se. Many inhabit the layers between cells in a balanced and harmonious relationship.

The fungi and bacteria that inhabit inside the plant cell can be considered an inside plant. These are defined as plants that grow inside the plants. These organisms can be beneficial neutral or beneficial depending on the conditions.

Plant pathologists have concentrated on pathogens or microbes which cause the deleterious reactions using a tunnel vision based on their training and focus. I can plead guilty to that focus in my professional development in early plant pathological work.

Nevertheless, the vast majority of soil microbes are either neutral or beneficial and not pathogenic as a pathologist bent would lead us to believe. Traditionally less than 5% of the soil microbes have ever been identified much less grown and characterized. The soil constituents a vast unseen treasure house and the majority of modern antibiotics for instance come from soil bacteria in the classification actinomycetes.

Many of the beneficial microorganism may have a soil phase but not grow in laboratory media and many of the Microbiologists have not wanted to study them for that reason. The vesicular arbuscular mycorrhizal fungi are good example.

If after surface disinfection a fungi or bacteria arise but is not associated with any pathogenic consequence it is considered an endophyte. Generally the plant material is submerged in 10% bleach and rinsed off and using aseptic planting technique in agar media the expressed microorganism are considered internal.

Identifying endophytes which stimulate plant defensive and health and nutrition is a emerging field of much interest. Hope this give some context to the Greek.

Paul, Whats your response. Why have we not able to exploit the plant endophytic microorganisms despite their utility so well expressed. Such microbes are perhaps metabolically more active than many of the rhizo microbes.

The term endophyte was first introduced in 1886 by De Bary ( De Bary 1884) for microorganisms colonizing internal plant tissues. Posada and Vega ( 2005) used the term endophytes for all those microbes inhabiting different  internal parts of plants, including seeds. Some commonly isolated plant endophytes have been observed to belong genera like Enterobacter , Colletotrichum , Phomopsis, Phyllosticta , Cladosporium ( PDF enclosed for further reading )  . The major application of plant endophytes include :  enzyme production , antimicrobial activity , source of bioactive compounds, biocontrol agents( endophyte fungi like Beauveria bassiana known as entomopathogens), nutrient cycling , bioremediation ( using microbial metabolism to remove pollutants through biodegradation ) . Hence, their functioning ranges from symbiotic to pathogenic (  Strobel et al 2004, J. Nat . Prod. 67: 257-268 )  .  Plant growth promoting bacteria are considered synonymous to plant growth promoting endophytes on the basis of their functioning ( PDF enclosed).  Many researchers claim such plant endophytes   predominantly as actinomycetes ( Gaiero et al. 2013 ,PDF  enclosed ) .

Such plant endophytes have been isolated from scale , primordia, meristem , resin ducts, leaf segments with mid-rib, roots, stem , bark, leaf blade , petiole, buds, and often from pollens of several pines of Mediterranean origin ( PDF enclosed for detaile d  information )   .

Hope Dr Deka , you must have found some of your querries

Rhizobacteria meaning rhizo root and bacteria can generally be used from the populations which reside in the rhizosphere the area influence by root exudation is about 1 to 2 mm in distance before its extinction. It is the root exudate that increases both the populations and diversity of these organisms. The soil is a nutrient deprived environment and much of role of this bacterial halo is because of exudations which can compromise about 20% of the total plant photosynthesis product.

The role of endophytes would appear less casual that most rhizobacteria because their internal nature stimulate plant defensive compounds. This is probably based on the ingress inside the plant triggering plant defenses. Plant defenses are systemic in their nature  not just affecting just the area around the root system as Dr. Srivastava ably points out endophytes can be found systemically in the plant tissue not just in the root zone surrounding roots..

In the case of the Claviceps fungi they are famous for their pharmacopia of chemical agents. In the related genera evolution seems to be taking them away for destructive visible disease roles into hidden colonization which works together in a smbiotic synergistic way.

Rather than resulting in seed destruction they evolve to stimulate a seed infection which increase yield and seed survival. Pathogenic chemistry becomes a type of plant steroid like system which deters predative insects, improves seed vigor and survival, deters pathogens and stimulates improved environmental reactions such as less sensitive to drought and other adversity.

The intimate symbiosis living together reactions are synergistic more than additive this is at the root of the great potential and utility of endophytes which may be greater than the rhizobacteria which are not necessarily endophytic and may live in a more causal relationships with Plants natures prime producers..

Paul, plant entophytes offer very promising potential, but my major concern is how to inoculate inside the plant or we have inoculate the plant rhizosphere.

Excellent response Dr Hani . What you have to say about the inoculation strategy of plant endophyte microbes other than AMs. What kind of mechanisms  operate to make them even more  effective than rhizocompetent microbes?

Only rhizobia play significant role as PGPR. But when we talk about other non symbiotic endophytes. Mostly they harbor plant tissue for shelter and there is no significance effect on plant growth and yield. If they have effect on plant. then how they effect plant growth? 

Dr Zaheer , I would suggest to go through some of the PDFs that I enclosed about the plant endophytes and the excellent response from Dr Hani . Hope , you find them useful . Let me admit , if you compare with microbial properties of  plant rhizosphere  or mycorrhizosphere , use of plant endophytes in improving the plant growth is still the most challenging task. On the other hand , AMs are genuinely endophytes , need living cells/tissues to multiply,  like any other symbiotic or non-symbiotic bacteria , irrespective of their source .

I am not an expert of this topic and feel updated with on-going discussion. Endophytes are alluring and considerable amount of work has been published. Several studies however do indicate reduction in herbivory in plants colonized with certain endophytes. At the same time there are some examples of endophytes that have been shown to be latent pathogens too (pdf attached). One should be cautious on use of endophytes. Koch’s postulate should be performed to prove the endophytic life cycle. The practical applicability to exploit the beneficial traits seems to be limited by inoculation technique and further expression of the inoculated endophytes as expected.

An excellent account of the plant endophytes  Dr Vinod Kumar  , you have given . There is absolutely no doubt , we have to exercise absolute caution while designating the isolated microbe beneficial to plant growth , duly tested through plant response studies . The earlier works done have claimed about the better effectiveness of endophytes over rhizocompetent microbes , however a lot need to be made clear at various levels of investigation . The biggest challenge emerges , with respect to their inoculation technique , in addition to warding off their  plant tissue specificity .  

In principle, what is the general concensus about the utility of rhizosphere microbes vis-à-vis plant endophyte microbes ? Where do they fit in safeguarding  dual responses,   plant nutrition vis-à-vis plant health?

Dr Srivastava Sir, Pathologist are often get skeptical with asymptomatic microbes. Though there are example of rhizosphere microbes used as bio control ( like Aspergillus niger stain as 'Kalisena' fior soil borne pathogens in specific crop ecosystem in India, atoxigenic Aspergillus flavus stain to contain aflatoxin contamination elsewhere in peanuts),  there should be studies about at what stage and in what circumstances the asymptomatic endophytes may revert to symptomatic causing harm to plants.

Nice answer Dr Vinod Kumar , do you feel such presence of microbes are crop phenology -dependent ? .  I am raising this issue with respect to developing  consortia of beneficial microbes ?. My another point of contention is , do you feel , a beneficial microbe  as an effective biocontrol agent will necessarily be a growth promoter? 

Can any one interact on the issues relating plant health management using such plant tissues derived endophytes, considered to be the part of plant metabolic sysyem.

Yes, I think endophytic microbes harness better plant responsiveness than free living microbes in the rhizospheres.

Endophytic microorganisms are reported to be present in internal tissues of  almost every plant  surviving on this planet earth . Md  Tofazzal,  I entirely agree with you  , the capacity of  endophytic microorganisms to colonize internal plant tissues of host plants has made such microbes highly useful to modern agriculture .

 Let me respond to Dr  Deka quarry about the use of endophytes for control of pests and diseases. Several examples are reported about the pest control . Most notable of all is the interaction between fungi ( entomopathogenic fungi ) and grazing grasses. However, Webber (1981) first reported on the possible utility of endophytic  fungi against beetle ( Excellent PDF enclosed for further reading on this issue) . Likewise control of plant diseases by endophytic microorganisms is mediated by specific metabolites secreted buy microbes 9 Life Science J. 2010: 7(2):57-62 , by Haggag , excellent PDF for further  reading  enclosed ). Hope Dr Ahmad Jaheer will be convinced with the massive utility of endophytic microbes.

My view on the query of Dr. Srivastava Sir: yes, I feel that though it may not be relevant in case of microbial consortia for rhizosphere application but for endophytes and also, if the consortia is to be applied as foliar application for disease management, crop phenology-dependent expression should be considered. And, beneficial microbe as an effective biocontrol agent may not be necessarily a growth promoter.

Nice update Dr Vinod Kumar , surely our learned colleagues will take some useful food for future thoughts on this issue.

 Dr Vinod  Kumar , it is often claimed that endophytes  utility could be more useful than rhizosphere- inhabiting microbes , since endophytes are not exposed to environmental extremes   and the unknown challenges posed by  millions of other microbes that harbor in the plant rhizosphere .  Applying consortium of endophytes through foliar spray  could jeopardise the very essence of the endophytes?. Therefore , inoculation of endophytes could  possibly put up a major challenge , with regard to harnessing their maximum effectiveness, and could be the major researchable issue?

I feel multiple inoculation of endophytes is possible, provided we workout the suitable inoculation technique. Shall it be inoculated inside the plant.

The case of multiple inoculation of endophytes is proven through the co inoculation of Rhizobia inoculant and mycorrhizal inoculant which in the tripartitate interaction with legumes is synergistic in its symbiosis.

The use of the combinations and technology is largely untapped in other areas however. As we study more, there will be opportunities unraveled and more other situations where the interactions is not so multiplying and even antagonisms. Hold on the ride should be breath taking.  

Nice feedback Paul let others respond to it.I steel feel there is long to go before endophtes are a reality

Paul you are right, but how to characterize the endophytes using the criteria used other than typical rhizobacteria.

I haven't found superiority of soil microbes compared to endophytes.

Plant growth promoting bacteria, phosphate solubilizing bacteria could better for study.

One can inoculate as seed coating or seedling inoculation.

Consortium of endophytes would be very much interesting, but one has to nullify antagonistic effects, if any among them.

I really need to know how  endophytes work as phosphate solubilizers inside the plant. As per thumb rule the soil microbes produce organic acid which solubilize the unavailable phosphate into available form and further making available to the plant. Similarly , the AM fungi as endophyte plays a role to mobilize phosphate inside the plant  through mycelia that is lying outside of  plant. But, where is the source of P (plant/soil) for endophytes ?? If plant or soil, what is mechanism ??

That's a very good point  Dr Upendra , I agree with you . Hope our colleagues will interact this latest issue. to my mind , the mechanism with AMs , I can understand , AMs mycelial network lying outside the host plants roots can solubilise the phosphate , take into their  arbuscules , and deliver it inside the plant, understandable . But  plant  endophytic PSBs , how do they behave , it will be interesting to know from our colleagues.

Upendra, I endorse your comments, Where from these PSBs bring phosphate for their substrate to be used in releasing inorganic P.

In the case of Piriformospora indica it is a mycorrhizal association but differs compared to arbuscular mycorrhizal fungi by being cultivated with ease in laboratory media. Being a Basidiomycetous fungus akin to Rhizoctonia like fungi Sebacinales it is phylogenetically separated from Arbuscular mycorrhizae.

Arbuscular mycorrhizae are obligate symbionts not grown on artificial media and having affinity to Zygomyceteous fungi. Very different in phylogeny yet it shares a soil habitat and adaptation to P. indica..

In both AM and P. indica there is an endophytic relationship in the root tissue and the fungal mycelium acts by extending into the soil.

The great increase in soil contacted and the ability to exchange nutrients in a balanced symbiotic relationship works in both these cases for P solubilization and movement I suspect.

The ability to easily cultivate P. indica and its remarkable ability to stimulate better ability to progress in saline soil and soil disease reductions have a lot of us very excited.

Saline soil is a big issue in semi arid and arid areas where the evaporation of water exceeds the precipitation from rainfall which is common in about 25% of global terrestrial area.

Dr. Biswas can you throw some lights in how to use isolated endophytes, just any other soil microbes.

Sikha

I have used isolated endophytes as seedling inoculation, seed inoculation and inoculated soil at about 108 to 109 cfu/ml

Interesting Dr Biswas, out of these inoculation methods , which one produced the best response.  I am  willing to know, do these endophytes behave the same way similar to typical rhizo-microbes?. Or do we have to find ways and means to make them more responsive

Dr. Anoop,

Seed inoculation was better with my study. It would be better for specific rhizo-microbes because their survival after inoculation is different.

It is frequently  claimed  Dr Biswas , endophytes if applied exogeneously  ( soil inoculation ) , might not be so effective since they will be exposed extremes of conditions , thereby , jeopardizing their survival rates?. Whats your take on this issue?

Dr. Biswas, how do you maintain colony count of such staggering count. It will be interesting to know.

I was  trying to find out some work  relating to  structural and  functional diversity plant endophytic microbes , similar to soil inhabiting microbes, but could not get . Can someone  share his/her experiences on this issue? 

Dear Doctor Srivastava

David Douds and Pamela Milner have a review of diversity in AMF fungi in the Rodale Farming Systems study in which 13 species were commonly identified based on spore morphologies.

The cover crops and organic amendments in the biologically based Organic Farming systems raised the populations of arbuscular mycorrhizal fungi and can be a mechanism of understanding their superior ability to achieve higher levels of soil organic matter over time.

The rhizosphere effect as you point out is one in which increased substrate from root exudation increases the size and diversity of soil microbes. The bulk soil seems to  Carbon limited.

Another way of looking at this is showing the extinction of soil organic matter as soil depth increases in the profile, the level and activity of arbuscular mycorrhizal show the similar pattern.

Populations and activities follow the organic matter this is why organic matter is so important. it serves as habitat and sustenance for the living microbial components.

Nice supplements , worth reading friends. Any other plant endophytes  Dr Hepperly , for example , bacterilal  species ?

Do you have any information on comparative efficiency of soil borne bacillus versus plant borne bacillus on any crop response ? Anyone of you can throw some light.

Dr Deka , so  far researches accrued on this issue , it is claimed bacteria of endophytic origin are more efficient compared to rhizophere origin , they are supposed to be metabolically more like a part of plant functioning . But , I wonder how to inoculate them ?. Shall we adopt soil inoculation or seed inoculation , very often seed inoculation finds difficulty in generating good plant response.

Dear Colleagues, Doctor Srivastava asks the question of how to establish the endophytic microbial populations most effectively.

Although a seed establishment is a best case scenario in my personal prejudice I also appreciate that  it can be fraught with difficulies. This seed capacity concern has led to the use of granules which are applied to soil near the establishing plant and give habitat and greater inoculum potential.

It is not unreasonable to see both of these as potential agencies seed and soil can be supplemented by liquid avenues through irrigation especially drip irrigation which has an advantage of targeting the inoculum to a region of concern could be useful and viable and not mutually exclusive.

One can easily appreciate how the engineering and mechanics can work with or against the biology. Since biology is more complex historically more attention is given to machinery which has an input that applied biological approaches which depend more on insights of the life forms involved.

This may encourage use to see the need and power for interdisciplinary team approaches to systematic issues for effective problem solving potential.  \

Unfortunately our academic communities are not designed thus and continue to foster silos of expertise. These silos work against what is needed to address critical complex issues that can face us.

What do you think?

What kind of differences in microbial diversity you can expect when it is compared with rhizosphere versus plant endophyte diversity other AMs. My second question is , do you need to have some domestication/hardening of endophytes before straightway inoculating in rhizosphere.

Dr Hepperly , very nice comments , appreciate of you . Application of  plant endophytes similar to conventional use of rhizo-microbes like seed inoculation , growing medium inoculation ( Soil inoculation ) and possible use through irrigation , surely hold promise.  however my  concerns and I agree with Dr Deka in this regard , on two accounts viz., plant endophytes are brought to an entirely new environment while using them through any of these three options as described above  , may restrict their efficiencies and number two , their compatibility with  different soil components and other abiotic stresses of an open environment . Will those endophytes resist these two possible consequences ? . Your thoughts please.

Dr Srivastava, very thoughtful querries you have put up. These are facts needed before endophytes become a practice.

I presume that there is no question of soil or endophytic microbe as an effective PGPR.... It is known that almost all the crops are harboring these PGPR in their rhizosphere and endophytic region. The so called PGPR/inoculants are being isolated only from these environs and in turn are being used as PGPR. My point is that it is immaterial whether the inoculant is from rhizosphere or endophytic origin. An effective PGPR should compete/over populate/effectively contribute than  the existing PGPR populations in the study environs and should beneficial to the plant growth

Yes in a way , you are right Ramachandran , but lot of  previous reviews and researches have claimed  endophytes are more  responsive than rhizosphere -based microbes, however both have PGPR ability .

Some rhizosphere are found as endophytes. Some of them even control diseases. One of BARI scientist reported that Bacillus oryzicola control major rice diseases and thus improve rice yield. I have found they produce IAA and improve photosynthetic efficiency in rice.

Thanks Dr Biswas  for very informative feedback , i appreciate your efforts . infact , if you look at the history of plant endophytes , it goes back to 1925-26 , when some reports started flashing about the competent plant endophytes  isolated from rhizoendosphere and phylloendosphere of a plant . infact , it looks to be more adventourous reading the history of endophytes than rhizosphere inahabiting microbes?. how do you feel , what could be the source of these micorbes which are colonising inside the plant  within endosphere ?.  Do you feel , some microbes inhabiting within the rhizosphere could invade through the root tips of root hairs , then they colonize and endure within the plant tissues ?

In terms of getting good inoculation it is a function of quite a few factors. The use of appropriate numbers and stages of the inoculum. The appropriate carrier and storage condition. The application of material not past their date. Appropriate environments post inoculation. When we inoculate mycorrhizae the harboring of the inoculum within a transplant with media and grown under appropriate conditions represent a best case system. Ideally the proper probiotic is not in need of amendment but is a consequence of a farming system that favors the biological potential because of soil husbandary. The soil environment many times is the problem and adding a probiotic is not as favorable as creating an environment which will foster the probiotic action without continuing inputs.

Dr Hepperly , thanks for an impressive   response and kudos to your articulative language . My simple quarry is , if  we get a Pseudomonas isolated from any part of the plant , do you feel , that Pseudomans will more effective to inoculate than the Pseudomonas isolated from rhisosphere ?. Which microbial diversity , shall we look now , the diversity within rhizosphere or diversity within endosphere ?

The origin of inoculant is not much important (either it is from the rhizosphere or from inside  plants) since all the endophytes today might have been migrated only from the soil source initially.  A successful inoculant should able to compete with native microbes and should outnumber them and also should efficient enough to contribute to the plant growth through BNF, growth hormone, biocontrol, enzyme activities etc...

 Thanks Dr Ramachandran fro your response , very interesting . Our quarry was , a microbe isolated as endophyte , has a better opportunity to compete with native microbes than the same isolated from rhizosphere , No doubt , the same has gone from rhizosphere only . But , the most competent one only will invade the root hair , go inside , colonize and endure . That was the point ...

Thank you very much for your response and the point is very very valid one.As  per your view that the competent strain alone can invade into plant tissues and survive and contribute. If it so, there is no need to inoculate another PGPR again.

Moreover, there is no concrete evidence to prove that homologous is superior than non-homologous though a few findings are available. Well, I have been conducting field experiments on sugarcane with homologous (area wise, variety wise) and non-homologous diazotrophs on sugarcane for the past 20 years. but could not arrive a reproducible concrete evidence that homologous strains are superior than non-homologous one though some results are positive for homologous strains.

Thanks again Dr Ramachnadran for an excellent counter response , worth appreciating . We can likewise  isolate  , characterize and develop into multiple inoculation mode with time to come . There could be some crops where such principles may or may not be so effectively operating . But , as a principle , i am talking . However, there is long way to travel with regard to endophytes?  . 

Dear Everyone,

Thanks so much for the update. I have learned a lot from reading this thread. My interests lie in seed endophytes. Documenting the endophyte community is not an issue. What I want to is- How do I remove the endophyte community ( bacteria and fungal) and still maintain seed viability. I am aware of benefits conferred by endophyte to the survivability of the seedling. My main objective is to produce axenic seeds for downstream experiments. A lot of publication that made reference to axenic seeds only mention surface sterilisation and seed embryo excision. I am also aware that the use or antibiotics and antifungal reagent will hamper the seed development and I am very weary of this method. Is there another way to get axenic seeds? 

Look forward to your responses. 

Thanks.

Thats a very good point Itumeleng. So far we have been concentrating on the isolation . characterization and development of consortium of endophyte s( If possble), besides their  biometric response on plant growth. 

We have not been addressing the issue of removal of  endophytic but pathogenic bacteria and fungi from seeds , without affecting the seed viability .I will be more than  happy , if any one can interact on this issue?

An excellent discussion Dr Srivastava. Let us concentrate our discussion on endophytes which act more like a regulator of plant growth than pathogenic ones. 

In terms of consortia I believe that mixtures are and will be of greatest value because of the problem of survival capacity. In plants if your have 6 or more varieties in a perennial crop such as alfalfa for example the safety is in the number of strains.

When the plant is perennial the sexuality of a cross pollinating one will allow both survival of the fittest but also the regeneration of an adaptive population of recombinants.. These same principles can apply to microbes also. 

In the case of both Rhizobia and mycorrhiza the use of mixed inocula has benefits which would likely mimic the case of synthetic populations of alfalfa varieties.

Many types of Pseudomonas species particularly the P. fluorescens species group have been screened for the growth promotion in plants and their antibiotic capacity for plant pathogen inhibition..

If  I were to develop this Pseudomonas tool for my consortia tool box I would search the literature for prime excellence of Pseudomonas working and tested under both field and laboratory condition successfully with 6 or 7 good example test them in mixture under diverse field conditions with appropriate controls and design for a hypothesis test.

If the Pseudomonas consortia is effective it might well prove out like the case of rhizobia and mycorrhizae that is if the farming system rotation and amendment is favorable the favorable components can persist and even increase in it. 

My gut feeling that soil competency of the target consortia is very important for this view and result. 

Many of the scientific community do not like mixed bag of organisms since it complication both the experimentation and interpretation.

Often when working compost for instance it becomes apparent that its power can be traced many times to it natural diversity in microbial sphere tand the process used. The convenience of a single mindedness can kill the power of  complex diversity when we look at improving something we might sacrifice details of knowledge for the end result. 

Case in point is the use of manures for mushroom production while these ingredients are not clearly defined the application in mushroom culture has consistently given superior results compared to the work of defined synthetic media. 

Some times the things we do not clearly understand are those that have the most power. For a scientific mind always wanting a simple explanation this is vexing to say the least. 

Yes Paul , while developing any microbial consortia , specific to any crop , the native soil environment will have to be borne in mind . Evaluating microbes in -vitro is quite different than evaluating their response in field . And , while doing so , we bring root environment as well , to complete the continum of soil-plant-microbe interaction .

In a summary Mr Srivastava composition of communities isolated from the rhizosphere (exophytes) and endosphere (endophytes) will differ base on specie plant likewise even their activities will be different i will refer to a work done by Berg et al. 2005  on a field-grown potato plants using a multiphasic approach. Terminal restriction fragment length polymorphism analysis of 16S rDNA of the bacterial communities revealed discrete microenvironment-specific patterns. To measure the antagonistic potential of potato-associated bacteria, a total of 2648 bacteria were screened by dual testing of antagonism to the soilborne pathogens Verticillium dahliae and Rhizoctonia solani. Composition and diversity of bacterial antagonists were mainly specific for each microenvironment. The rhizosphere and endorhiza were the main reservoirs for antagonistic bacteria and showed the highest similarity in their colonisation by antagonists. The most prominent species of all microenvironments was Pseudomonas putida, and rep-PCR with BOX primers showed that these isolates showed microenvironment-specific DNA fingerprints. P. putida isolates from the rhizosphere and endophyte gave nearly identical fingerprints confirming the high similarity of bacterial populations. The phlD gene, involved in the production of the antibiotic 2,4-diacetyl-phloroglucinol, was found only among Pseudomonas isolates from the rhizosphere and endophyte. Evaluation of the bacterial isolates for biocontrol potential based on fungal antagonism and physiological characteristics resulted in the selection of five promising isolates from each microenvironment. The most effective isolate was Serratia plymuthica 3Re4-18 isolated from the endophyte. and like am working on a legume plant and considering the exudation of root exudate by legume and the mutual relationship that exist between the plant and rhizobacteria definitely exophytes.

Thanks so much Ibrahim for an excellent response. Well said , thats the point , we are emphasising , micorbial communities of rhizosphere and endorhiza  possess some kind of similarity in  their structural and functional behaviour with regard to not only antagonism , but growth promoting ability as well, which formed the very basis of this whole discussion . Legumes by the virtue of inbuilt mechanism of nitrogen fixing ability , are  much better  equipped to facilitate microbial diversity ,besides secretion of root exudates. but b, most important is to study the defining functional niche between exophytes and endophytes..?

Anoop,

To reiterate your observation on the importance of soil based symbiosis. When we go from a straight grass permanent pasture to a straight clover pasture not only is the "requirement" for Nitrogen fertilizer unnecessary but in addition the soil nitrogen increases with the soil carbon and the number of earthworms multiples several times.

The legumes are the nutritional bastions and they fuel the whole system from the ground up. Nutrition is from the ground up and the air down. 

We need to look to legumes because they through the symbiotic relationship feed the soil that feeds the plants and animals. Plants animals and microbes are designed to work together in unity and synergy. 

Thanks Paul , i appreciate  the intensity of your discussion and flagging some thoughtful issues , which surely , w e need to lay some emphasis in years ahead.  No doubt , legumes have such a profound effect , either as  a cover crop or as a part of cropping system , in either role ,  legumes are  so indispensable in nutrient cycling vis-a-vis soil health resilience .  

We need to work more on the synergies emerging out of rhizosphere and endosphere vis -a-vis  different crop including legumes so that microbial profiling of different soils can be carried out in relation to that crop.