Phytobiomes Alliance & USCCN webinar 01/25/2024
Presenters:
Matthew J. Ryan, CABI, UK
Nicola Holden, Scotland Rural College, UK
Jacob Malone,John Innes Centre, UK
Tim Mauchline, Rothamsted Research, UK
Outline:
Culture collections, involving the accession and supply of microorganisms in pure culture, have long supported microbiological research. But how can collections and biobanks in association with data networks support and underpin the ever-evolving fields of microbiome and phytobiomes research? This is just one question we will be addressing in our webinar, using the example of the UK Crop Microbiome Cryobank, a project seeking to preserve, characterize and utilize the microbiota associated with 6 key crops – wheat, barley, fava bean, oat, oil seed rape (canola) & sugar beet. We will discuss
i) how you can preserve a ‘microbiome’ and the methodologies applied to conserve functional potential and ensure sample integrity,
ii) the benefits of building a focused, utilizable resource,
iii) how we add value through genomic characterization and analysis,
iv) how we share data to our user community and link it to EBI resources such as MGnify through http://AgMicrobiomeBase.org and
v) how we are utilizing the resource as a blueprint to develop sustainable Nature-Based interventions for crop health.
Finally, we will discuss how the model used for biobanking can be expanded to other crop types and holobiont systems, and how a biobanking approach is essential not only for industrial and academic research but also for capturing biodiversity to allow for future mitigation against climate change.
www.agmicrobiomebase.org
Slides of the presentations can be downloaded here: http://tinyurl.com/ytfy9z78 or http://tinyurl.com/52et33ab
Hello everyone and welcome to the phytobiomes alliance webinar series we have a great um webinar for you today um and just to begin um I’m going to go through a brief introduction so my name is Dusty Gallagher the project manager for the International Alliance for phytobiomes research of the phytobiomes
Alliance and I’d first like to thank all of our phytobiomes Alliance sponsors that you see here on the screen without their support we would not be here today and so the generous uh contributions by those that you see on the screen um are what makes the phyto boms alliance um what it is
And the success um of our Consortium and so the International Alliance for phytobiomes research is a nonprofit pre-competitive research Consortium we’re composed of members from industry Academia and government and our overall goal is to create a paradigm shift in agricultural research and production it is our vision that um by
2050 all agricultural producers would have the technology um think of them in a field with a handheld device that will allow them to determine the best combinations of crops management practices and inputs for a very for a specific site in a given year and this information would be supported by predictive and prescription
Prescriptive analytics based on geophysical and biological conditions so the strategy of the alliance to meet this vision is to identify the gap in research tools and Technologies and develop project teams and research projects to address them so just quickly a phytobiomes is a plant that is growing in a
Particular substrate and so in this infographic you see soil but it could also be a many different kinds of of substrates that the plant grows in and then that system that f phytobiomes is then impacted by many other components whether it be um microbiomes and microorganisms animals plants insects
Climate weather water and all of this is influenced by management practices so again the phytobiome strategy is to identify the gaps um Within These components and then move agricultural research uh to a systems approach based on this phytobiome so here are just a few examples of phytobiomes we typically
Think of crops growing in soil but it could also be pastures vegetable gardens forests vertical farming or any type of controlled environment Agriculture and a subset of the alliance or an alliance project that is also co-hosting this webinar today is the US culture collections Network and this
Network is a you NSF funded research coordination Network that is designed to bring together scientists who work with collect isolate living microb Collections and this is a partnership with the phytobiomes alliance and one of the major focuses of uscn currently is to build a public registry of uh microbi collections so
Think of this as a sense of of microbes and so we’re reaching out to those researchers uh the academicians even Private Industry who have any microbial Collections and we’re asking them to input some information into an online registry and this information is crucial to um those that wish to use these
Valuable resources and um also could be very helpful um in um the commercialization of some new products developed by by these microbes and this is voluntary information and it’s housed on the uscn website and I’d like to bring your attention to one of the main activities of the phytobiomes conference that will
Be held this year in St Louis October 8th through the 10th and that’s our International phytobiomes Conference and this really is the culmination of all of the information and projects of the phytobiomes alliance and so we will be discussing and hearing some wonderful presentations from uh multidisciplinary
Research work on a number of different topics and we’ll also be continuing this webinar series um so stay tuned for more information uh about upcoming webinars so I want to thank you for your participation the websites of both of the groups the phytobiomes alliance and
Uscn is here on the screen and will also be added to um the uh information that you will see within uh Zoom today and so please follow us on all on all of our social media channels and that’s a great way to find out information upcoming by these
Organizations and so today’s webinar I’d just like to go over um the rule Rules of Engagement um this webinar is being recorded and will be posted on the pho bombs Alliance and the uscn YouTube channels later today and uh just a bit overview I know everyone is very familiar with the zoom
Platform but um during the presentation um as you’re hearing from these speakers if you have any questions or comments we would like to invite you to submit these in the Q&A panel that you will find typically at the bottom of your screen and then um if you monitor the chat um
Portion of Zoom then you will see some messages um from the organizers of this webinar and then in the handout section will be links to the websites will be PDFs of the slides given today um and other information for you so just remember for your for the Q&A that that
We will have at the end of our time please submit those questions in the Q&A panel and then if you haven’t already we invite you to register to our mailing lists to receive news about upcoming events um and that link will also be posted um in the uh chat panel so
Without further Ado I would like to welcome our panelist today who will be um discussing the UK crop microbi iome cryobank a utility to support phytobiomes research and today we have um Matt Ryan with cabie in the UK Nicola Holden Scotland’s rule College Jake Malone from the John inis Center and Tim
Ban from rothamstead research in the UK so we would like to welcome all of you to our webinar today and they will be tag teaming the presentation so I will turn it over to Matt Ryan who will begin thank you very much Dusty on behalf of Tim jnick and the whole G Bank
Team we’re very grateful for the opportunity to present this webinar today so in this presentation we will look at the background of why we need to preserve and and store material to support phytobiomes research I’ll give you a little bit about the project the partners and the ambition of the project
And our approach to cryobanking and then I’ll hand over to Tim Nick and Jake as we look in more detail about how we generated the resource and how we’ve in fact um characterizing it and ultimately utilizing it for the future so to start we need to really
Assess where where we are now as a global Community culture collections have long supported microbiology research but they generally only store xenic cultures that is culture stored in pure format very few culture collections actually store more complex samples be they microbial consortia or the actual microbiome environmental samples themselves biobanks are another um
Really important facility but they have been quite different in their operation from culture Collections and typically they would only either store dead or fixed material such as museums or viable seeds or medical related um resources currently the the the world has some 793 culture collections represented some 3.2 million strains in
17 77 countries and regions across the world and we’re all familiar with some of these larger collections in the states for example the American type culture collection and in Europe the Wester Dy and dsmz we also have cabie my own collection that I’ve been it’s been
An honor to create for many years and that has a as a global for um focus all this is underpinned by national and Regional networks such as the United States culture collection Network and in Europe the European Confederation of culture collection abbreviated as Echo but what where does a need come
From well that’s started initially in 2015 at a uscn meeting in Fort Collins Colorado when professor Jan leech um challenged the assembled culture collection experts to support fighter biome research at the same time there were was an initiative starting in the UK between rothamstead and cabby um called the UK
Plant microbiome initiative and that was promoted through the rothamstead open Innovation Forum aligned with this was a development in Europe with the formation of the microbiome support project which the phto biome Alliance was associated with so why do we need microbiome biobanks they’re roughly the same reasons that we need culture collections
Is to Aid the development of Standards to allow deposits to ensure compliance with legislation in including the ngoya protocol as a source of new potential products for industry medicine and environmental applications to protect intellectual property such as storage of sycom or live bio biotherapeutic products for biodiversity conservation
And to mitigate against future threats but ultimately to provide resources to underpin the very stringency of research and it’s also important to recognize that there is a purpose and need for biobanking we’re not looking for looking to preserve samples as a stamp collecting exercise our goal is to add
Value to the resources we collect while characterizing an art asking key biological questions about the resources that we C curate at the start of the European project that I mentioned earlier we held a workshop in Austria and we looked at the supporting infrastructure for fighter biomes and microbiomes more
Generally and the issue was the microbiomes were falling through the Gap they weren’t being covered by biobanks they were only Loosely being covered by culture collections and the the large European infrastructures didn’t really cover them specifically and this is an opportunity to mention an EU project that is
Brilliantly led by Tanya cotic in in at the Austrian Institute of Technology um where we looking across domains not just in the plant microbial area but also in the marine and human areas and this is entitled an RI enabler so this is the link to ensure that the research
Infrastructures approach this in a in a validated way and hopefully this will be an opportunity for a um another webinar um in the future so why do we want to preserve microbiomes and what’s the aim obviously we can preserve and store actual cultural isolates and the aim is
To do that without change to their gen genomical physiological Integrity we can store the nucleic acids but the real challenge comes in storing environmental samples and we we we want to store them in a format that allows micros to be recovered from them at a later date um and that is really
Key because we don’t know what technologies will come along tomorrow to allow us to do that another really important factor is that microbiomes are Dynamic so we’re only looking at a snapshot in time but we’re still looking to retain the viability genomic stability and functional potential of of those samples and that’s incredibly
Important if you want to maintain activities for future biological applications so this is where the UK crop microbiome cryobank came around about it’s funded by the bbsrc and it looks to establish a comprehensive platform to facilitate research towards optimizing plant yield in an integrated crop management framework it is focused
On key UK crops they are wheat oil seed rape or Ola as is known in the states barley oats sugar beet and beans and it is a collaboration between five institutes the John inis Center rotham did research cabby the James Hunton Institute and Scotland’s rural college
And it’s important to note that we can not have undertaken the project without the key collaboration of those institutes the project is structured around four separate work packages firstly it’s a collection and production and culture of samples and Tim will tell you about that in a few moments the genomics and bioinformatics
Which is managed by Nick and then the actual physical cryo bank that is located at cabi in egum in the UK and soon to be moved to a new s at silwood Park in barkshire and then finally the utility of the resource which is being managed by Jake
Malone we’ve approached this using two pooling methods so we take the samples and we’ve applied a control rate cooling method this is a standard method used by culture collections for for preserving axenic microbes that will capture most three thre tolerant organisms and we’ve backed that up with an encapsulation vitrification approach
Which will hopefully and we know it does actually capture the more delicate and freeze ralen organisms for our actual cultures we’ve used a high throughput approach and that’s really important because we we can handle 96 cultures per run rather than one in an ampul and that’s led to a
Physical resource that’s now complete over the course of the last three years we’ve we’ve preserved 4,800 individual PRI viles um by both of the methods that represents not only bulk soil and riser plane samples but we’ve also validated that with 36 culturable isolates in 36,000 culturable isolates in micro
Titer plates um and that is a huge resource the actual cabby collection is only 30,000 strong we we’ve almost well we have increased that over the course of the last three years and we know that our preservation methods work I can’t go into more detail because this work is subject to
Publication um but effectively if you preserve a microbiome you can recover microbes afterwards we have a lot of data that we’re looking at in the moment but obviously more research is required and that’s something that the EU project is looking at as well I’m now going to
Hand over to um Tim Morlin who’s going to talk to to us about how we’ve actually generated the resource and how we’re functionally characterizing it over to you Tim thanks a lot Matt okay yes as Matt said what I’d like to do now is is tell tell you all about what we’ve actually
Done to build the resource so this really is has come about from um a large sampling campaign across UK um field soil types and what this has been built on is the the knowledge from a previous project which was called the assist project and uh and
From this there was a large array of different soil um types that were available so what we’ve managed to do in this study is actually go to the the assess the data for these different um soil types from these different Farm um um locations and from there what we wanted to do was
Actually generate and collect the the soil from these different some from a subset of these locations and what we wanted to do was make sure that we did this from across um the the whole area of the UK so as you can see according to
The the map on the right there where we have is a a cluster of of three um points in the in the north um including Scotland some in the West towards Wales there and then also in the the southeast and the idea being that each of these
Three clusters contained an example of a sandy soil a clay soil and a silty soil and so what we’ve managed to do is build this entire resource of nine different soil types and the the idea being as Matt’s already touched on is that we’ve we’ve used um um important crops for um
UK agriculture so this is actually six um different crops um and then we also have box oil controls and for each of these um we’ve we’ve then collected collected the soil from these and actually done this experiment which is the whole basis of the resource so
Thanks man so is this here is an example of the some of the the pot experiments that we’ve done and and you can see on the left there the the nice different um colorations of those different soil types so this is um demonstrating the different soils that
We actually did sample and on the right there there’s some examples of the different um crops that we’ve grown so just to recap we focused on wheat UL drape barley oats sugar beet and beans and as I mentioned also there is um the bulk soil controls and what’s quite nice
Here is we’ve manage to to have a range of different crop types so we’ve got cereals brassas as as well as legumes okay next slide please ma’ okay so what we’ve been able to do in this um experiment is as I mentioned it’s a large pot experiment it’s actually based on
315 different um samples and this is because of the nine different soil types um and five replicates of each um crop that we’ve written including the the bulk soil as well and so what we’re able to do is generate these bulk soil and risos spere samples and from from those we’ve then
Generated a large microbial culture collection and uh and in addition to that we’ve also performed DNA extractions on the um the bulk so and riser samples themselves to do a culture independent analysis and this has allowed us to do amplion sequencing to to get some taxonomic information using
Both 16s as well as its on a subset of the samples which is the the beans and the the wheat samples we’ve also done metagenomic um shotgun sequencing and actually on the the bacterial isolates themselves as Matt mentioned we had 36,000 isolates that we’ve we’ve generated from this project
We’re currently undergoing a um a barcoded indexed identification of those all 36,000 in addition to that a subsets are being whole genome sequenced and so as you can see there are multiple types of sequencing data that being generated from the whole Community to the individual isolate and all of that
Information is being collected and will be put into the the appropriate repositories as indicated on this figure next slide please M so what I want to do now is tell you a little bit about some of the work that we’ve been doing on these isolates so just reiterate we’ve got 36,000 isolates
And what we we’ve done is is screen them all for um a a range of different functional um tests and what we’ve done is we’ve broken this down into atic stress tolerance so this examples of that are ACC damin production the ability to um tolerate salt stress and also to deal
With drought stress in addition to that we’ve looked at micronutrient um um the ability to actually solubilize micronutrients or capture micronutrients in the case of um ion via steri production as well as zinc solubilization and furthermore we’ve also looked at the um the ability of these isolates to solubilize and hydroly
Macronutrients so we have an example of organic n as well as um phosphorus um solubilization in terms of example there being tricalcium phosphate as well as potassium solubilization and the preliminary data that we’ve gleaned from this so far has been quite interesting so what we try to
Do is as you can see on these three figures here if we look at the the one on the left you can see that we’ve we’ve um colored all of the um the points according to the actual site and what we found there was actually quite difficult
To actually see any real trends and then if we look at the figure on the right hand side this was then by the the soil cluster if you remember from the previous slides that this would either be a silty a Sandy or a clay soil so they were the three different cluster
Types again it was quite difficult to to actually um find some clear Trends but what we we were interested to see was that when we actually look in the the central plot there we could actually see some Trends according to um crop type so what we were able to see really was that
There are um some clustering according to the serial type and the seral as in serial crops with the the actual bacteria that were isolated from those seem to be clustering together based on their phenotypic profiles whereas we see for sugar beet as well as beans for example that these are separating away
From the actual cereal type okay so next slide please M okay so the next thing we want to do is tell you about the actual um frequency of functions per crop so just to reiterate we see all the different functions that we’ve screened for here
So as I mentioned there th those to to do with um abiotic stress tolerance there’s uh macronutrients and micronutrient solubalization and the three standout results that we’ve seen from this data so far is that n hydrolization seems to be reduced in isolates which have been um uh isolated
From the bean Rises sphere and whereas we can see for the um the the drought um um function the isolates that have come from B drape and sugar beer more prevalent whereas we see for zinc um there is actually a large increase in the um number of isolates which have
That um zinc solubilization function from barley so it seems for in terms of beans I mean I think there’s a good um for me there’s a clear reason why they would actually be reduced in the um in the Bean system due to the um the the the the plant’s ability to form
Mutualistic symbioses with ryia so there isn’t such a huge requirement for that function it’s also interesting to see that um in the Ed rape and um sugar for in terms of drought tolerance due to the the larger root systems it could be that this is um and reflecting the the actual
Um the Thirsty nature if you like of ory rape and sugar be Roots regarding the The Barley that’s more puzzling and I don’t have a clear explanation to why barley has a um an increase in zinc solarization but that’s something that we’re currently working on to understand
Next slide please Matt okay so before I pass on to Nick what I want to do is just summarize this part of the talk which is just to show really what resources for Downstream analysis that we have now generated so as I’ve already said this is a resource based on six key
Crops and in addition to that we also have the bulk soils this is uh this has come from well characterized soils this is this a cyst Network I mentioned but in addition to that um we also have a couple of examples of um soils which have come from the James Hutton
Institute as well as rotten stead Farms the data types that we’ve been generating are in terms of amplion sequencing just to re TR 16s and it shotgun metagenomics we also have a lot of soil metadata that’s um what that’s why we chose these particular um sites
In the first place we are we actually managed to achieve um the actual isolation of 36,000 um whole isolates and um as I mentioned we are currently barcoding these isolates um and that’s in progress and as I mentioned there there there’s also some key fun that we seen and
Finally just the last Point really is that we see that individual isolates typically have limited functional range so that we didn’t see many isolates which have the broad plethora of functions they more um Limited in their different functions okay I’d like to now pass over to Nick thank you very much
Tim for that introdution okay so um I’m going to now describe what we’re doing in work package two and um here uh Tim has already described this first slide and this is really an overview of uh the sequence dependent data that we are obtaining from this
Project um so one of the points that really I really want to make about the project um oh hi you can see me now um is that we are collecting a lot of different sequence types as as Tim had mentioned um but what we want to do
Obviously is put them into uh the public archives and so that they are accessible to everybody and we’re working with the European uh nucleotide archive um which is run by emble and also their um repository that they have for microbiomes which is known as magnify um but what we are generating as
Part of this project is an an access portal and I’ll describe that to you next slide please thanks Matt okay so there’s a lot of detail in here and I’m certainly not expecting anyone to read the detail but the point that I wanted to make is that this is actually quite a complex
Experimental setup so you saw what it what it physically looked at like in the um glass houses at rothamstead H but one of the key points is that we have a lot of really important metadata as Tim had mentioned that these um sample were collected from a a research project for
Which we know quite a lot of the heritage of the fields for example we know a lot about the um physical and the chemical nature of the soils um and all of that metadata is really important for understanding the influence that the microbiomes might have on the crop
Production system so we have and taken a lot of time and ATT paid a lot of attention to this metadata and made sure that it has all been captured um and so it provides an incredible rich source of data for interrogating the sequences and next slide please
Matt thank you okay so where are we putting it all um now uh we’ve got this really nice little website that we’ve got up and running um and you can find the the web address there a microb bias.org so what it is it’s an Open Access Data catalog um in terms of its
You know technical ability of how what will house and how it can be accessed so what we wanted to do was to make it an interface to integrate query and visualize the sequence-based data and that very important metadata that I mentioned as well um what it does do is
Give direct links to the sequence repositories that we’ve got like um Ena and magnify um but I should say that this is currently in development this is very much in development so at the moment what we have is some of the 16s amplion data in there and we have a very
Nice example for spring wheat and I’ve shown you some of the um the outputs in tabular form and some of the graphs that are associated with that as well and what I would like to point out is the funding source for our this project um has a funded other similar projects so
We are generating a biological and bioinformatics resource and we have lots of other examples of um other projects under the same funding scheme where they have developed something really quite spectacular um and I’m really pleased to see that you know what we are doing very much aligns with the the trajectory of
Some of these other um projects that are funded in the same scheme so uh yeah watch the space for developments for a microbiome base H next slide please and now what I’m going to do is just show you a couple of the data outputs um that we have here I’m not
Going to go into too much detail like the others but just to give you uh flavor of what we’re getting and it’s pretty powerful so since we have such a large data set um and robust data set we’re getting some very very nice information and what these different
Colored um shapes and symbols are showing you is that we’ve got very nice um taxonomic uh diversity within our total sample set um and what we’re showing here is the divers or the diversity between different samples so we can compare one against the other for example and see how similar or different
They are and this just gives you a nice flavor for that um taxonomic diversity and this one this example was based on the 16s for all of the different crop types in all of the different soil loal combinations next slide please and what I’ve done here is I’ve
Just taken the data for just one of those crops so this is sugar beat and what we can do with the data for example is not just look at the taxonomic composition but we can also um look at the um the actual uh variation within or the microbiome sorry within a particular
Crop uh so what we’ve got is um just one crop sugar beat and we can compare different uh soil type locals and we can see um where those similarities are and where the differences are and again you know this is focusing on the 16s amplicon so this is looking at
Taxonomies that are similar but I should mention a really important Point here as well so I think this is where um we’ve we are generating a very rich data set because what I’m describing here is the 16s amplion or the taxonomic composition data but you’ve already heard from Tim’s talk um
That we have got uh different sets of drivers that are differentiating on the isolate basis so this is um a really nice example of why it’s important to look at these different scales whether you’re looking at the whole uh Community composition and what’s driving that or whether you’re looking at the individual
Isolates and what’s maybe driving the function of those okay next slide please okay so our next step um as Tim mentioned is we’re also doing shotgun metagenomics um on a select set um so again we have all Soil local combinations for two different crop types and then no plant control so we’ve
Just acquired um these raw data sets just now so we’re at that very exciting uh stage of just pressing the submit button and then generating the functional data and we are working very much with um emble ebaa uh emble I beg you pardon um on the outputs for this um
And this is their pipeline um again unless you’re very technically minded this probably won’t mean anything to you but I think there’s a little animation if you press next please please Matt yeah so what we’re going to focus on is really the functional part of this P
Pipeline we can get a lot of information from that sequence-based data um and then we can ascribe different functions and that of course relates back to the actual functions that have be measured in rothamstead as well and in johnan is what you’ll hear about next um next
Slide please so I’m just going to finish up and just say that um one of the key things that we’re doing is we’re generating a large number of different data types and they’ve got all of this Rich metadata so a big job next really is to try and integrate these um so
We’ve got um an example of some of the soil types for examp uh here um I’ve also listed the soil chemistry um we’ve got the community compositions we’ve got the actual cultured isolates and then we’ve got the functions as well so there’s a really big job I think to do
Now is to try and integrate that so you can actually get you can ask much bigger strategic questions about the data set and really what we want to do with this resource is not just provide that Baseline information for the community but to you know to get them involved um
It will enable you to do comparative analysis with your own data sets for example we can do the compare and contrast for those different functions we can look at where the taxonomies might lie and that have specific functions as well so I think it’s an incredibly exciting stage that we’re at
Um and I’m looking forward to working with the community more on this sort of data integration and thanks I’m gonna hand over to our colleague now in John Andis Jake right hello um thanks I’m just checking that my videos come up uh thanks everyone for um com to this um my
Section really is just to um to talk about how we would use all of this information I think my colleagues um have done a fantastic job so far in actually generating um The Cry bank and all of the genetic material and biological resources underpinning it
What we want to do in in uh John inis is to show how um the Cryer Bank can be used uh can you move on to the next please thank you uh so what we want to do is to produce synthetic Comm communities and to show how those synthetic communities can contribute to
Plant health and plant growth and ultimately this should provide a case study for how the microbiome project can be used by um all stakeholders really because ultimately what we want from this uh collection is for it to be um active and for it to be used it
Shouldn’t just be um something stored in a freezer we would hope that the community will um use the website will’ll use the collection in order to um to to um pursue agricultural projects so um first of all in order to to produce these sycom the first thing
We need to do is to um produce um well to to understand the culturable microbiota within our samples um much more than we do and there’s been a tremendous amount of phenotyping done um by rothamstead already but what we would like to do is to understand the plant growth promoting
And biocontrol traits a bit more of the cultural collection we then want to go on and um from a a very large um broad um characterization we want to move on and test some positive plant growth promoting traits of individual microbes within the collection and next please
M and ultimately we want to use this information to create effective growth promoting synthetic communities so the way that we’re going about this in a bit more detail uh next slide please um I’ve broken this down into a number of different steps um the first thing we have done is to take
Thousands of isolates from the um the freezer collection and we are just checking the viability of those isolates if we reculture them obviously they were cultured in the first place but they have been through the freezing process and not all of them um well some of them may not have
Survived so we’re doing in the first uh stage a a very broad check for isolate viability we then go on and apply a number of De different phenotypic tests um in a high throughput manner looking for plant growth promoting traits biocontrol traits and morphological traits Associated um with success in um the synthetic
Community from these different screens we go on to choose a range of isolates with different abilities that we hope will contribute to a successful synthetic Community um we’re carrying out genotyping and whole genome sequencing of subsets of these isolates and then ultimately we’re putting together collections which go into plant growth
Promotion assays in controlled microcosms we’re also um down down the line once we’ve done these steps we intend to do metabarcoding of our syncom to show how the communities will change throughout growth in different plant environments and how the distribution and abundance of different bugs within the synthetic community may change and
Next slide please so this is just giving a few examples of the the work we’ve done so far this is very much um ongoing work um but we’ve done a lot of viability checking and I’m pleased to say that almost everything that’s been recovered has grown um you can see here these are
Isolates from um bean and from wheat growing on either sand or clay oh or isolated from Sand or clay soils and you can see almost everything is growing and after 48 Hours um we see a substantial amount of those isolates grow robustly I should say that the um the
Isolates which are shown as not growing here it’s not that they don’t grow it’s just that they grow slowly but it’s quite interesting that we are seeing quite a lot of variability between our different samples next please we’ve also conducted as I said a number of different uh phenotypes uh
We’ve looked at things that we would associate with effective bio control or effective uh growth promotion for example um we’re looking at proteo production here using milk eggar plates and again you can see huge variability between the different sample sets that we’re looking at and next please we’ve also started work on gen
Typing the culture collection so this is identifying the nature of the individual um microbes from the 36,000 isolates that um the Matt mentioned earlier so um this is a very early stages I should say inconclusive on this this chart doesn’t mean that those bugs don’t have a
Genotype it just means we haven’t got on to genotyping them yet but what’s interesting at this stage is that we see um quite a sort of variability but we also o see quite big differences between for example the bean and wheat um microbiota that are associated with clay
Soil um with more Cris of bacterium and billus found with wheat and pseudomonas and Pen bacillus found with Bean it would be interesting to see how this pans out Across The Wider collection um next slide please so as I said this is the workflow that we’re currently working through um most of the
Um the work is is probably still on the the first four of these boxes although um all of them are more complete or some of them are more complete than others um I should just finally say a couple of words um about the plant growth promotion assays in microcosms and how
We intend to to conduct these going forward so uh next please so the way that we intend to do this is using a system called um the ecofab 2.0 system which was a developed um in the Berkeley Laboratory um by Trent Northern and his group and this is
A model lab ecosystem that allows for highly repeatable uh plant growth results so rather than growing in um sort of Jerry rig systems that we um we put together ourselves what we would like to do and we’ve been working in the last year to get this system up and
Running um here in Norwich is to um next please actually um if you click for a couple thank you um what we would like to do is to use these EAB 2.0 um growth Chambers uh which are reusable growth Chambers where plants can be grown with their root systems in a highly defined
Environment um and this will enable us to conduct highly repeatable plants growth assays uh we’ve tried this out it hadn’t been used for crop plants before uh this project but we’ve successfully grown both barley and wheat and one or two other plants at this stage um in
These systems and we’re now able to conduct all our experiments we hope um in highly reproducible conditions so what we intend to do is to inoculate um these plants with our different synthetic communities and measure plant growth um over a defined time period and next please so the next steps um for this
Project um obviously we we’re going to continue and complete the Gen typing next um and to conduct more in-depth phenotyping and ultimately this will allow us to move on to implanter assays and our strategy here is both to examine how uh synthetic communities contribute to the health and growth of individual
Plants but also and next please how the microbiota associated with one plant for example Bean or a second plant for example wheat next please how those two distinct microbiota will um differ in their abilities to promote plant growth if we were to swap them over um as Tim was
Saying earlier we know that the functional traits associated with these different microbial communities uh really do seem to be driven by the plant species itself so were we to make a a swap um next please and swap the um the Bean microbiota for the wheat or vice versa
Next please then we would hope to see um some interesting differences in terms of their abilities to promote plant growth so the um final thing to say for me really is is to move on and summarize the uh the whole project so at this stage we we have a number of key
Conclusions um we can say that the the cry Bank thus far has been uh highly successful um we hope it’s going to both a utility and a model for supporting phytobiomes research going forward we’ve shown that you can successfully um preserve soil samples and retain almost all of their functional
Diversity we think it’s a really unique resource um which links physical samples with Provence data genomic metadata and ultimately functional data and these samples have been stored um in publicly available um and well-known um well-known data banks the resource can be interrogated to answer biological questions and the work
In my lab we’re hoping to provide a case study for this and to provide some best practice um really to to enable people to um to ask questions going forward we can also say we’ve um identified some interesting um biological pointers already from the work that we’ve done in
Creating the the resource for example that drivers of community compositional variation are different to um that apply to iser function and I guess I would finish um by saying that preserved characterized biological resources such as this uh can provide promising leads for future development um in the production of nature-based solutions to agricultural
Problems so uh next please I’d finally like to end by acknowledging all of the people um associated with this project um the team um on the The Cry Bank are Tim Morlin U Matt Nicola Holden and myself who you’ve heard of heard from today also Ian Clark
Sue Jones Rodrigo um tatani pton Yao Helen Shu Stewart um Miguel Bonin K Thompson and um the support teams at our different institutes we also have an excellent scientific Advisory Group who um have been providing us with pointers and steering the project um over the last few years this is Tom Bell James
Prer D belli Cara Haney Ruth bastel Susanna Bolton L Shaw kellou Rob Finn and Gina swart um we also have input from Imperial College from Tom Bill and Tom Tom Bell and Tom Lily and from ebi with Rob Finn and te and I’d like to thank um
Everyone for listening and we’d be happy to answer any questions thank you um to our panelists and our presenters today um what a great project and a and a great um set of work that um that you’ve presented and that um we can all um look forward to it progressing so
We have about 10 minutes for some questions and we do have a number um of questions that have already been submitted um so I will just begin um some of them have been identified to a particular speaker and some um are just general questions so one or all of you
Um feel free to answer so um to begin um the first question is for Tim and it is was isolate screening done and high throughput and if yes did you publish these methods or protocols um yeah thanks for the question um yes what we’ve been doing is we have we
Haven’t actually published it yet this the um the actual method is is still um is is will will form part of the main publication that comes from it but essentially we’ve been using Robotics and um that’s the way we’ve been sort of uh um us getting the isolates to be
Organized but there’s been a lot of essentially um hard work in getting the isolate collection made but then the organization is through robotics if that makes sense okay thank you um a question that is not um pointed to anyone in particular but are there crossovers in species composition between microbes
Found in the plant and microbes in the soil where they grow should I have a go with that one okay well no no you go next one or I can’t yeah no um we yes we definitely see some differences so we have a nice demonstration of what we term or what we
Understand as the rise of feere effect so that’s where you get um enrichment of particular groups of microbes um from the soil so the soil is the source of the microbes um onto the plant um but that doesn’t happen in the same way for every plant species so we do have plant
Species dependent effects as well on top of that but yes we do have demonstration of the risos spere effect does that answer the question I believe so yes thank you okay another question for Tim how many indexes can be used in a single run are there any limiting factors with the
Indexes and what could be the ways to modify indexes to optimize the runs so there’s probably about three questions in there um let me know if you would like any of that repeated no I can actually see the question it’s fine I think that my um my colleague rodri
Rodrigo takatani would be best place to answer that question actually um so so yeah I’ll have to get back to you on that one unless Nick you want to unless is that indexes for sequencing um in which case we used the 96 um Multiplex system for each
Run if that was the answer to the question I’m not sure I’m not sure if it’s referring to the the culture independent or culture dependent sequencing yeah okay okay so maybe we’ll do a followup after the yes please yeah absolutely okay um so um one of the
Attendees says I am not familiar with these resources do you offer workshops or trainings that students can attend and are you planning to make it as on online resources to run or is mainly scripts yeah I I’ll tell that one yeah we plan to publish all our protocols
Training is something that we’re all absolutely passionate about um and that would be a followup to this project and I’d also like to mention the EU micro biobanking enabler project as well that’s run out of AIT because as a key component of that project is training um
And that will cover a much broader Spectrum than just plant and soil it will cover the marine and and the human as well so there will be much more coming in this area not just from this project but from other projects as well and to follow up with that Matt um
I um failed to mention another effort that um is a very big collaboration um in Europe as well as in the US and that’s the microbes for climate project in which habby and the phyto bombs Alliance and uscn are involved with um and so you know there
Seems to be a number of these collaborations and projects in the works um and do you feel that they’re all related and can all work together um and perhaps you could just briefly describe the microbes for for climate project as well yeah absolutely collaboration and networking has been key to culture
Collections ever since I’ve been involved with that um and it’s going to be key in this field as well because no one organization can do everything um and not only can one organization not do everything you need those collaborators to bring the bioinformatics expertise to bring the characterization expertise to
The Wider Consortium and so there definitely needs to be um be more networking and I guess what we’re doing is trying to show a model and we think this model is applicable to other crop systems as well so we’re we’re focusing on the key UK crops but you can take
What we’ve done and we think you can apply it to to um commodity crops such as cocoa and coffee or or or other crops such as Ma so we think there’s great great potential for that um and of course one of the things that Jake’s doing at the moment is he looking at
Developing um sycom for future intervention and one of the big questions that faces the world at the moment is the impact of climate change the impact to drought and what is happening in the soil and the plants that accumulate those microbes and we don’t know enough about it so the micro
For climate project again is an EU project that’s bringing some of those things together but it will also extend to looking at the Regulatory and the legal side of things as well so the the work package that I’m leading there is is not so much on the Practical it’s
More on the the the ethics the legislative side of it and also the best practice and again this comes into some of what we’ve been discussing today because there is a need to biobank and preserve samples and it’s not not just to have a a sample at the end of it is
To make sure you adere to regulatory processes whether you’re in the UK the states or anywhere else in the world and that is a really important thing that we have to do as responsible microbiologists thank you Matt so our next question is have you done any experiments that address how microbiome
Functions vary over time and if so can you tell us a bit more about those experiments I can have a quick go at that if that’s okay yeah um it’s yeah thanks for the question I mean that’s something that we’re quite interested in doing at the moment at rothamstead we actually have a
New um field experiment which is is actually designed to answer that question so what we’re um doing is we’ve just made this new uh what we called cropping transitions experiment where we are going to be having lots of different um cropping rotations and uh and the
Idea being that we will actually also be doing um intra season samplings so we’ll have a we’ll be able to get some more information on that we have done some work in that um sort of Zone if you like in the past but uh but there was more
Detail required that’s why we were actually designing this new experiment anybody want to add to that Jake you were I was just going to say in in the um the context of the uh sycom experiment well we we do intend to do a lot of these experiments in a a defined
And highly we hope as reproducibly as possible so we compare we can compare across different samples we also um would like to look at for example the longevity of um samples how they um like the stability over time so if you grow a plant for 3 weeks or if you
Grow a plant for a month or two months or three months do you see differen in in how the synthetic Community will will maintain its stability so um it’s certainly something that’s on our radar although we haven’t undertaken it yet okay maybe time for one or two more
Questions so um our next um says what was presented was ambitious and impressive but at the same time likely Limited in scope based on region crops and number of samples could you please describe what the scale would look like to optimally conserve the ideal optimum number of microbes uh phytobiomes nationally
Regionally globally how would something like this be implemented and funded um and question was addressing the goal of global conservation okay you should have a go at that to start with because that’s the million dooll question um yeah we had to start somewhere as a proof of principle
And that is why we focused the resource on the key UK crops and that was a requirement really of the fund and we had to show it was utilizable and as I said in one of my early slides it’s not just about collecting microbes for the sake of collecting microbes you have to
Do it for a purpose and a reason and what we’re showing here is as you add value to them you can really ask some absolutely amazing biological questions who pays for it um I think that is a community discussion to have obviously for research funders when you consider
How much they invest in research the cost of maintaining these collection is actually very small and I think we all have a duty as researchers to make sure that we make our um results of our out research outputs available to to other workers because without that you can’t
Test the stringency and you certainly can’t reproduce any results so it’s really fundamental to very existence of science from a conservation perspective um yeah who’s going to pay to to conserve everything but you could for example narrow that down and look at keystone species for certain groups so
There’s lots of possibilities we need to have a discussion with the community and that’s where the fighter biomes Alliance the uscn and our EU collaborators really come into to answer that that broader question great thank you very much and I just want to say again we are at the top
Of the hour um and so I just like to thank all of our panelists today for joining us and giving us an excellent presentation thank all of the attendees for joining and we do have a number of questions um that we didn’t get a chance
To answer live and so we will ask the speakers to follow up um um to answer those questions so thank you very much for attending look for our next webinar to be um in March and we’ll be sending out information um about that soon so thank you very much have a great day