How to attract Cyanobacteria?

How to attract Cyanobacteria?

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I would like to attract cyanobacteria in one spot on an object (e.g. cloth,) instead of having it swim in the media. my current method is to pour it on the object in a beaker and wait for some of them to become attached (very pour attachment yield).

Now, I am thinking of making the object emit light. Do you think that the bacteria will swim all the way to the cloth because there are attracted to light?

is there a better method to help the bacteria get attached to the cloth?

It might work, many cyanobacteria are reported to be phototaxic.

Chapter 11 - Cyanoomics: an advancement in the fields cyanobacterial omics biology with special reference to proteomics and transcriptomics

Cyanobacteria are most primitive photoautotrophic prokaryotes, including diazotrophs blessed with specialized nitrogen-fixing cells, that is, heterocyst. Photodiazotrophic nature of cyanobacteria enables them to fix atmospheric nitrogen, as well as carbon in paddy fields. Notwithstanding this fact, these photosynthetic prokaryotes have always attracted the attention of researchers due to applied usage in several areas such as biofuel, biofertilizers, and biotech industry. However, photodiazotrophic nature makes cyanobacteria the most attractive model for basic science researches such as developmental biology. Furthermore, the availability of complete genome sequences of cyanobacteria makes their stress adaptation and developmental processes feasible at transcriptional as well as translational level. Unfortunately, till now, only 85 fully sequenced cyanobacterial genomes have been available on databases, and most of the sequenced genomes comprise a significant portion of uncharacterized proteins (>50%) with unknown functions.

Moreover, genome sequencing leads to the foundation of functional genomics, which encompasses the study of vivid and dynamic changes in genes, proteins, and their interaction networks. This chapter attempts to unlock the true potential of these cyanobacteria by the study of functional genes at the level of genome, transcriptome, proteome, and metabolome. The study via functional genomic opens up new and fascinating aspects of understanding the functioning of various genes and proteins of cyanobacteria, which could in turn prove beneficial for various biotechnological and industrial applications.

Cycads: Life History and Ecology

Interactions with other living things, or biotic interactions, play an important role in the biology of cycads, particularly in pollination, seed dispersal, and the acquiring of nitrogen nutrients.

Cycad pollination was long thought to be a chance event, effected only by the wind. This was especially troublesome for understanding the success of understory cycads in tropical forests, where there is little wind, and where pollen studies have shown that there is almost no cycad pollen in the air. More recent investigations have suggested that beetles, especially weevils, and small bees may make a more important contribution to the transfer of pollen. Studies have also shown that some cycads at least will produce heat or odors to attract these animal vectors.

The seeds of cycads are quite large, and are often brightly colored red, purple, and yellow seeds are common. These colorful seeds are displayed as the cone matures and the seed-bearing leaves separate from each other the colors attract birds and a variety of mammals which disperse the seeds.

One of the more novel biotic interactions among plants is an association with photosynthetic bacteria, such as Anabaena. In cycads, the cyanobacteria are sheltered in specially modified roots which have the appearance of coral, and so are called coralloid roots, as seen above at left. These roots grow up out of the soil, rather than down into it, and are thus exposed to light which the cyanobacteria need. In return for providing this stable habitat, the cycad acquires nitrogen nutrients from the bacteria.

Cycads grow in a number of tropical and subtropical climates.

Though they are often among the larger plants in their environment, cycads are no longer abundant or dominant components of the world flora. Today's cycads are found on every continent except Europe and Antarctica, but are restricted to a limited number of areas in the tropics and subtropics.

Cycads grow in a number of different habitats. Species may be found as components of the forest understory in both rainforests and seasonally dry forests, or occasionally as members of the forest canopy. Other cycads grow in loose stands in grasslands, forming a kind of savanna. Exceptional among the cycads are species of Encephalartos, one of which is visible at right, which grow in eastern Africa at very high elevation. Here they must contend with extremely xeric conditions -- low rainfall, harsh winds, and dry soil -- and must deal with frost and heavy snow at times as well.

Many cycads may be grown outdoors in California and the southern United States, but they cannot seem to tolerate the less equable climate in other parts of the nation.

Many cycads face imminent extinction.

Today only a handful of cycads still exist, and many are facing possible extinction in the wild (such as Microcycas in western Cuba). Cycads are in danger of becoming extinct both because they live in endangered habitats such as tropical forests, and because they grow so slowly and reproduce so infrequently.

Several species are already extinct in the wild. Many more are under threat from habitat destruction, and pressure from unscrupulous collectors. However, because of their large attractive leaves, many cycads have found a home in public and private gardens around the world. Breeding programs at several institutions have been undertaken to preserve the various species, but this is made difficult by the necessity of maintaining genetic variation present in natural populations. To protect natural populations, five genera are now covered by international law, prohibitting trade of seeds collected in the wild.

All this effort may not be enough to save the cycads from extinction. Fairchild Botanical Garden in Florida maintained one of the world's most comprehensive collections of living cycads, including many that are endangered in the wild. The Garden was severely hit by hurricane Andrew in 1992 and most of the non-native plants, including most cycads, were severely damaged or killed. A botanical SWAT team from Missouri Botanical Garden was helicoptered in to Fairchild as the storm clouds were clearing. Their goal was to save as many of the plants as possible, and to preserve the rest for future study.

How to attract Cyanobacteria? - Biology

The cyanobacteria are a fascinating group of bacteria that have adapted to colonise almost every environment on our planet. They are the only prokaryotes capable of oxygenic photosynthesis, responsible for up to 20-30% of Earth's photosynthetic productivity. They can attune their light-harvesting systems to changes in available light conditions, fix nitrogen and have circadian rhythms. In addition many cyanobacteria species exhibit gliding mobility and can differentiate into specialized cell types called heterocysts, and some are symbiotic. Thanks to their simple nutritional requirements, their metabolic plasticity, and the powerful genetics of some model strains, cyanobacteria could be exploited for use as microbial cell factories for carbon capture and storage, and for the sustainable production of secondary metabolites and biofuels. Understanding their cell biology is an essential step to achieving this.

In this book, leading senior scientists and young researchers review the current key topics in cyanobacterial cell biology to provide a timely overview. Topics covered include: historical background cell division the cell envelope the thylakoid membrane protein targeting, transport and translocation chromatic acclimation the carboxysome glycogen as a dynamic storage of photosynthetically fixed carbon cyanophycin gas vesicles motility in unicellular and filamentous cyanobacteria cellular differentiation in filamentous cyanobacteria and cell-cell joining proteins in heterocyst-forming cyanobacteria.

This cutting-edge text will provide a valuable resource for all those working in this field and is recommended for all microbiology libraries.

"this resource offers up-to-date information . presents the fundamentals as well as what is currently known and being researched, providing the grounding for further progress" from Book News June 2014

"I recommend this book to every student and scientist working with cyanobacteria and I am certain that it will still be read in ten years time. " from Biospektrum (2014) 20: 827-828.

This review summarizes the current knowledge of the chemical properties and structure of glycogen and starch-like reserves in cyanobacteria, the different enzymology and regulation of glycogen biosynthesis and degradation, and the function of glycogen metabolism in cyanobacteria. A special focus is drawn on its roles in photosynthetic efficiency, during the process of nitrogen chlorosis and for the steady-state of anabolic and catabolic reactions, especially under unbalanced growth conditions.

7.5 kDa) is a metamorphic protein, adopting two conformations in an asymmetric dimer. These assemble into an amyloid (i.e., open-ended, cross-&beta) ribbon that wraps around the vesicle axis in a shallow helix and presents an aliphatic face to the interior. This aliphatic face is expected to cause evaporation of liquid water from the interior of nascent vesicles and prevent water condensation inside mature vesicles. A second protein GvpC, adheres to the GvpA shell and strengthens it. A great deal remains to be learned about how other members of the gvp gene cluster cooperate with the two main structural proteins in assembling and disassembling vesicles. Of particular interest is the fact that, despite the amyloid properties of the vesicles, the cells are able to dismantle them, in order to descend in the water column and apparently recycle protein from vesicles that have collapsed.

(EAN: 9781908230386 9781908230928 Subjects: [microbiology] [bacteriology] [environmental microbiology] )

Cyanobacteria and Microalgae as Sources of Functional Foods to Improve Human General and Oral Health

In the scenario of promising sources of functional foods and preventive drugs, microalgae and cyanobacteria are attracting global attention. In this review, the current and future role of microalgae as natural sources of functional foods for human health and, in particular, for oral health has been reported and discussed in order to provide an overview on the state of art on microalgal effects on human oral health. It is well known that due to their richness in high-valuable products, microalgae offer good anti-inflammatory, antioxidant, antitumoral, anti-glycemic, cholesterol-lowering, and antimicrobial activity. Moreover, the findings of the present research show that microalgae could also have a significant impact on oral health: several studies agree on the potential application of microalgae for oral cancer prevention as well as for the treatment of chronic periodontitis and different oral diseases with microbial origin. Thus, beneficial effects of microalgae could be implemented in different medical fields. Microalgae and cyanobacteria could represent a potential natural alternative to antibiotic, antiviral, or antimycotic therapies, as well as a good supplement for the prevention and co-adjuvant treatment of different oral diseases. Nevertheless, more studies are required to identify strains of interest, increase overall functioning, and make safe, effective products available for the whole population.

Keywords: Chlorella vulgaris Spirulina platensis Streptococcus mutans antimicrobial activity microalgae oral health.

Transcript of the episode

ALISON : Hey! I’m Alison Takemura, and this is Genome Insider, a podcast of the US Department of Energy Joint Genome Institute or JGI. Our intern and my fellow science communicator, Ashleigh Papp, is kicking off this story.

ASHLEIGH : So, billions of years ago, the world was a really different place. How then did our planet go from uninhabitable to a biological oasis, primed for life as we know it?

ALISON : The answer? Cyanobacteria!

DEVAKI : I thought about this, and then I think a nice way to say it is to put you into a time machine. And go backwards in time. So if you think about it human beings have been here about 200,000 years. So that’s not the kind of time machine I’m talking about. I’m not talking about a 65 million years ago dinosaur time machine. I’m talking about two billion years ago. And that’s when cyanobacteria were already hacking it. And that’s pretty phenomenal.

Devaki Bhaya in the field, 2008. (Research Coordination Network)

ALISON : That’s Devaki Bhaya, a plant biologist at the Carnegie Institution, at Stanford University. She studies cyanobacteria and how they interact with their environment and other microorganisms.

ASHLEIGH : These tiny little creatures, cyanobacteria, are photosynthetic. This means that they use sunlight to produce water and energy in the form of fixed carbon. They were the first organisms to produce oxygen, and we know that because of these fossils called stromatolites. These were formed by layers of cyanobacteria over 2 billion years ago.

ALISON : Without these little organisms, we probably wouldn’t be here.

DEVAKI : It sounds very grandiose and it is because before that … the earth was anoxic. There was no oxygen. So these guys actually oxygenated the world.

ALISON : And it turns out we aren’t the only lifeforms to benefit. A whole host of other organisms often live alongside cyanobacteria, taking advantage of the valuable resources that they provide.

DEVAKI : Bacteria don’t live alone. And so, almost always they’re in communities. And I think that’s going to be the great new frontier that all of us are interested in is, how do communities work together.

ALISON : On today’s show, we’re talking to scientists who study cyanobacteria and look for clues in their genomes about how they’re evolving and how they’re interacting with other microorganisms.

ASHLEIGH : Devaki and her team are trying to understand how cyanos — as the researchers like to abbreviate cyanobacteria — are living in their microbial community. They want to know how they’re changing on a genetic level, and, why?

ASHLEIGH : To study how cyanobacteria interact in their own little communities, Devaki and her team set out into the field to collect samples. They traveled to Yellowstone National Park, in the northwest corner of Wyoming. But, despite the park’s beauty, I don’t think they could’ve picked a more extreme environment to sample from!

DEVAKI : I was thinking, the first time we went to Yellowstone it was like walking into what has been described as what hell might look like. It’s hot, it’s sulfur, you know, it’s dangerous. There’s boiling mud. And I mean, it was unbelievable.

ALISON : They chose two different sites: Mushroom Spring, which is a flat, steaming pool surrounded by reddish brown dirt, and Octopus Spring, which lives up to its name … it has a big bulbous central pool surrounded by off-shoot pools that look like tentacles. Both springs are filled with freshwater that’s heated by magma deep below the earth’s surface.

ASHLEIGH : The average temperature of the water is hot to even hotter: from 60 to 90° Celsius, or 140 to 194° Fahrenheit.

ALISON : Oof, that’s hot!

ASHLEIGH : So, the cyanos in these pools are known as extremophiles, or lovers of these extreme conditions.

The terraces of Mammoth Hot Springs are made of soft limestone and are constantly changing shape as water flows. Note: this area was not studied by Devaki and her team. (NPS / Neil Herbert)

ALISON : Because they’re so hot, these pools are similar to life on earth some two billion years ago. And, in more recent years, both of these pools in Yellowstone have been well-studied by other scientists. So baseline information already existed, helping this project get oriented.

DEVAKI : For all of the audience who’s listening to this, I would say: go there because there is nothing that compares with seeing that environment and how varied it is, how difficult the terrain is.

ALISON : But the cyanobacteria are not the easiest to get to.

MICHELLE : You have to hike in to actually go sample.

ASHLEIGH : That’s Michelle Davison. She started working with Devaki in 2006 while getting her PhD.

ALISON : Devaki and the research team wanted to sample the cyanos throughout the day to see how gene expression might be changing. And, one time, when Michelle was out at 2 AM … well, she was fine, but …

MICHELLE : I got a little lost on the way back. And I didn’t have my bear spray. But everything worked out.

ASHLEIGH : And the springs that Michelle had to hike to? Are absolutely breathtaking.

MICHELLE : It’s this beautiful bubbling cauldron of blue that eventually like fades to green as the temperatures cool down and the cyanos start to grow.

The bright, clear blue waters of Emerald Spring, in Yellowstone National Park, mix with yellow sulfur deposits to give off a bright green reflection. Note: this area was not studied by Devaki and her team, which cannot be shown in accordance with National Park Service policy. (NPS / Jacob W. Frank)

ALISON : The spring water itself is a light, clear blue, and the green around the edges of the spring are made up of the cyanobacteria. The cyanos live with and above other layers of organisms, and together they form what’s called a “microbial mat.”

MICHELLE : So the mat is kind of like a rubbery texture. It’s because these organisms create all these polysaccharides and create this matrix.

And when you take the samples you are taking a core borer, actually, and you’re taking a sample of the mat, a plug of the mat. And it looks like one of those very fancy desserts that you would get in a high end restaurant, and you have all these layers and layers and at the very bottom, you have this charcoal gray layer, which is the sediment that’s there. And then you have these layers of orange.

ALISON : These orange layers are dominated by two genera of bacteria, Roseiflexus and Chloroflexus. According to Michelle, these are cyanobacteria’s “lazy friends,” because they get all of their nutrients from the photosynthetic cyanos. All of these different organisms live together in a microbial community.

MICHELLE : And you can see that there’s that community structure…. So it’s a very appealing system to look at.

A slice of the mat core sample. The top green layer was used for metagenomic and single cell sampling. (Devaki Bhaya)

ASHLEIGH: You know, the sample that Michelle took of the microbial mats kind of reminds me of a dessert that my Grammy used to make out of Jello. She would start off by making one flavor, and then layer in other flavors and colors on top of it … in the end, a piece, with all of its colorful layers, looked just like a rainbow!

But it’s not Jello that we’re talking about. These microbial mat samples are made up of living organisms and probably not nearly as tasty.

ALISON : Each microbial mat environment can be unique, and the nutrients that get exchanged within it also vary depending on who’s there and what’s available. But, in general, the cyanobacteria on the top use sunlight and carbon dioxide to produce oxygen and fixed carbon. The cyanos also fix nitrogen, pulling it out of the air to make it usable. Other members of the community harness these diverse nutrients .

ASHLEIGH : Another member in this microbial mat community are cyanophages. Phage means “to devour” in Greek, and these cyanophages prey on, or infect, cyanobacteria. We’ll get to more on them a little later, but for now, you should know that they’re a part of, if not necessarily invited to, the microbial mat party.

ALISON : Once Michelle and her colleagues had collected core samples of the mats, they packaged them up, kept them frozen with dry ice, and then shipped them to their lab at Stanford. In the lab, Michelle took some of the samples and began working on isolating and growing cyanobacteria. But she quickly realized that she had traded in the challenges of the field, for new ones at the bench.

MICHELLE : So one thing to remember is that these organisms that we’re working with are just several generations out from the wild. They’re basically — they’re not model organisms. They’ve been taken from the mat. And we’re culturing them in the lab. But they’re still very much an unknown and a wild animal.

ASHLEIGH : This means that Michelle had to experiment with new tools and techniques. One example had to do with getting the wild cyanobacteria isolated.

MICHELLE : Because these cyanos are the primary producers of the community, getting them clean or away from heterotrophs that want to stick with them, and actually literally stick to them, can be difficult . So one of the tricks that we used was using phototaxis.

ASHLEIGH : Heterotrophs are microbes that, unlike the cyanobacteria, can’t fix carbon to make food for themselves … and they try to mooch off the cyanobacteria. So, because cyanos are photosynthetic, Michelle realized she could separate the samples by using lights to attract the cyanos — kind of like a magnet attracting lead filings.

MICHELLE : And they would leave their friends or parasites behind and move towards light.

ALISON : Remember when we said that we would come back to the idea of cyanophages, or viruses , in the microbial mats? Well, now is that moment. Michelle and Devaki are after all the genetic information that they can get about the microbial mat community. And now, that includes information about the viruses. But their investigation didn’t start out this way.

ASHLEIGH : Viruses came into the picture, when the team’s initial sequencing data turned up something called CRISPR.

ALISON : CRISPR, which is short for clustered regularly interspaced short palindromic repeats, is the bacteria’s adaptive immune system. CRISPR is made up of short sequences from viruses that the bacteria have encountered in the past, so that, next time, they can recognize and neutralize these viruses. A remarkable feature of CRISPR is that the snippets of viral DNA are stored — like books in a bookshelf — in the order that they’re encountered. They’re like a historical record of infections.

ASHLEIGH : CRISPR was first discovered in E. coli in 1987, but it remained largely a mystery until the mid-2000s. It was around then that Devaki and Michelle found CRISPR arrays in the microbial mat bacteria. And at the time, the team didn’t know the significance of the arrays or what to do with them.

DEVAKI : B elieve it or not, we actually found these and we put them on the back burner because we didn’t know what they were. And then the world exploded when the whole CRISPR story came out. We started looking into it and trying to figure out, well, this is telling us a story.

ASHLEIGH : The bacteria had wildly different numbers of viral snippets, called “spacers,” which are nestled in between the CRISPR pieces. Here’s Michelle:

MICHELLE : When we looked at the genomes … there was an interesting contrast between the cyanobacteria and the Roseiflexus and Chloroflexus bacteria. They had CRISPR arrays that were very, very long like some of the longest, 700 to like 700 something spacers, where the cyanos had like, 100. So these two living side by side, it was clear that they had very different interactions with their phage even though they were living in the same environment.

ALISON : Devaki thought that the CRISPR virus sequences could lead them to clues about how cyanos and their predators interact.

DEVAKI : It’s a little bit like a fishing hook, those little pieces allowed you to say, if I find this, I can kind of figure out who the partner virus is. So it quickly brought us into an arena that we were not experts in, which is to understand host and phage relationships.

ASHLEIGH : So, they decided to expand the scope of their experiment. Devaki and her team embarked on a journey diving deep into the interactions of the microbial mat community, viruses included.

DEVAKI : We will now, not just be able to do it just for cyanophage, but for the entire community, get a sense of who the viruses are and how they are changing. This is kind of an arms race, right? The virus is changing, the host is trying to change. And we can try to understand that in a much more detailed way. Where does the virus tend to mutate, where can it not afford to mutate. And I think that would lead to a much deeper understanding.

ASHLEIGH : Because Devaki and Michelle wanted to learn about how the viruses and cyanos were interacting, they needed a lot of data. Normally, that would be a limiting factor. But JGI’s Community Science Program helped to remove that barrier.

DEVAKI : So that Community Science Project allowed us to really expand the kind of data we wanted to collect. And what was fantastic about it was there was no limit to what we could ask for.

ALISON : Now, they’re looking for genetic clues in a seemingly bottomless pool of data.

DEVAKI : Now we have the ability hopefully over the next three or four years to go into a lot of depth and use different data sets to ask questions. And I think, therefore, bring a lot more detail and more insights into what looks like a simple community, but it’s far from simple.

ASHLEIGH : To try and understand what’s happening on a genetic level in these complex communities, Devaki and her team asked JGI for three different types of data sets: metagenomes, single cell sequencing of microbes, and viral genomes. And the advances in sequencing technologies were almost too good to be true, resulting in way more data or “sequencing reads,” than they expected.

DEVAKI : We had asked for, um, 50 m illion reads, something on that order for each sample. And when we got the sequencing back, Brian called me up and he said, you know there’s something wrong here.

ALISON : She’s referring to Brian Yu, who’s a Research Scientist at the Chan Zuckerberg Biohub. He’s on Devaki’s team and was helping to process the sequence data sent by JGI. On the phone that day with Devaki, he said,

DEVAKI : We have 400 million reads. I’m sure they’ve done something, you know, they’ve mixed up our— something. It turned out not to be the case, because that’s how many reads they get out of standard run now. So it was almost eight to 10-fold more than we aske d for.

ALISON : So, Devaki, Michelle, and their colleagues began investigating the 400 million reads of data — generated from the Yellowstone microbial mat samples just so far. Currently, they have metagenomic data, a survey of the total DNA in the microbial mat. With all of that genetic information, Devaki and Michelle had to figure out how to organize everything.

DEVAKI : Once we got the data. I think it threw up a whole bunch of challenges. Some are which are, you know, really how do you work with such large databases. But the second question was, how do we start to share data, and how do we as biologists start to really make sense of this.

The milky color of Porcelain Basin hot spring in Yellowstone National Park is due to siliceous sinter mineral deposits. Note: this area was not studied by Devaki and her team. (NPS / Jacob W. Frank)

ASHLEIGH : The researchers were sitting on what they called a treasure trove of data, thanks to JGI’s Community Science Program. It turns out, there’s another DOE resource out there to help.

DEVAKI : And it was a bit of serendipity. I was at the JGI annual meeting and there was an afternoon, and they said, you know you can join if you’d like to come listen to what KBase has to offer.

ASHLEIGH : KBase stands for Systems Biology Knowledgebase. It’s a Department of Energy, Office of Science-funded organization. KBase is a cloud-based platform to help scientists analyze massive amounts of sequencing information, like the kind you would get from JGI.

ALISON : The KBase team worked with Devaki and Michelle to set up a 4-hour workshop to learn about their project and how KBase might help in the analysis of the massive amounts of sequence data that JGI had generated.

ELISHA : We went over for part of a day and worked fairly intensely with her lab, specifically on their data, just to understand what their data was, what kind of questions they had about their data, and what the ultimate sort of science question was in terms of how they wanted to look at the analyses.

ASHLEIGH : That’s Elisha Wood-Charlson, the User Engagement Lead at KBase. She has a PhD in marine science and spent years studying microbes in marine environments. She’s on the KBase team helping Devaki and Michelle to analyze their data from JGI. For the KBase team, it was fun to dive into the sequence data of microbial mats.

DYLAN : Devaki’s system is fantastic. It’s one of these settings that’s perhaps representative of early earth conditions, right? And so that’s why these hot Springs are so appealing as a system of study.

ALISON : That’s Dylan Chivian. He’s a microbial scientist and coding engineer at KBase. With Elisha, he’s a part of the group that’s providing resources and tools to help Devaki’s team analyze the microbial mat data.

DYLAN : Her focus on the cyanos really gives us a glimpse into what those conditions might have been like for, you know, the chemical transformation of earth. So it’s fascinating just from a pure investigation into nature itself.

ALISON : And not only that, but these cyanos are interesting from a biotechnological perspective,

DYLAN : Because of their ability to operate in these extreme conditions, thermophilic conditions and so on, they wind up having very interesting chemistries.

ALISON : To get into the mechanisms behind the chemistry of cyanobacteria in the microbial mats, Devaki and Michelle started with the metagenomic data from JGI, which had been organized, or binned. They tried out different ways of re-organizing the data to yield the most information possible, and eventually they got to assigning assembled genomes to certain organisms.

ASHLEIGH : KBase works like a lot of other cloud-based tools — you sign in with a username and password, and are taken to a dashboard page. You can start working on a new Narrative, which is like a step-by-step recipe that shows how you analyzed your data.

ALISON : You can think of KBase like a recipe book — you write down directions to make all of your favorite dishes, record the perfect times and temperatures, jot down the ingredient proportions that you’ve tested out, save different versions, and, then, when you’re ready, share them.

ASHLEIGH : For Devaki and her team, the option to share all of their steps and information with other scientists is really helpful.

DEVAKI : We have collaborations that are across countries. So we have a group in the UK. And the question is, how do we all share this data in an effective way? And KBase, I think, allows that. That’s one of the, what I see as a big advantage. It’s like sharing your notebooks but with data — and big data.

ALISON : That kind of transparency can help accelerate fundamental discoveries, which is good, because as Dylan puts it, with this kind of sequencing…

DYLAN : We’re talking about trying to understand the genetic potential of earth. And we just started scratching the surface of it.

ASHLEIGH : KBase is a platform that accelerates genomic analysis through crowdsourcing. And when researchers are ready to share their work, those analyses can be made available to everyone, in real time.

DYLAN : So that it doesn’t take us, you know, a hundred years to start to have a picture of how the earth really works. It’d be nice to have that a little sooner.

Black Pool, in Yellowstone National Park, once contained cyanobacteria but now is too hot to maintain this life form. Note: this area was not studied by Devaki and her team. (NPS / Jacob W. Frank)

ALISON : The pace of the coevolution, or the arms race, between cyanos and their phages is still a mystery. Now, the virus samples are being sequenced and the team eagerly awaits that data.

DEVAKI : The questions we ask can be much more reflective of the kind of things we care about.

ALISON : In addition to learning about cyanobacteria and their phages, the team is also hoping to explore how the system, the whole microbial community, is evolving.

ASHLEIGH : Fundamental research, like figuring out who’s there and how they’re adapting over time, can lead to unexpected discoveries that determine how these organisms could be harnessed in a lab or used as a model system. One example that the team discovered in phages were genes encoding lysozymes, an enzyme that the virus uses to hack through cyanobacteria cell walls.

MICHELLE : One thi ng that is really hard about cyanos is they are hard to break open. They are super hard to break open. … a viral lysozyme that’s been evolved in order to be able to lyse these types of cells, might be a very good tool that we could use in moving cyanos to be more of a model system, or in using them to create some sort of high value product.

ALISON : One example of a high value product? Biofuels. Because cyanobacteria fix carbon from sunlight, they produce carbohydrates and oily lipid molecules that could be used instead of fossil fuels. Breaking open their cell wall like a piñata would help release those goodies. Admittedly, Devaki may be a little biased, but she thinks cyanobacteria are kind of underappreciated by…

DEVAKI : …the Department of Energy. Cyanobacteria should be on their flagship, actually, because they do so much.

ASHLEIGH : Right now, Michelle is a scientist at the Pacific Northwest National Laboratory. She’s translating what’s been learned about microbial mat communities, to soil. Yep, it turns out that viruses are shaping the lives and genomes of microbes there too.

Understanding tiny little microscopic things, like viruses and microbes, helps us understand so much more about the world around us. But in a general sense, we know so little about viruses — like, how they work, or why they do the things they do. And the COVID-19 pandemic is yet another example of our lack of information. The outcome of Devaki and Michelle’s work takes us one step closer to understanding more.

ALISON : For Devaki, harnessing the resources at JGI and high tech tools like KBase, is opening a future filled with potential for new discoveries about cyanobacteria and their communities.

DEVAKI : I’m just absolutely excited about what the next year or two is going to bring in terms of us putting together all of this information into insights that we really didn’t have before.

ALISON : This episode was directed and produced by me, Alison Takemura and JGI’s intern, Ashleigh Papp, with editorial and technical assistance from Massie Ballon and David Gilbert. Ashleigh was the lead writer on this episode.

ASHLEIGH : Genome Insider is a production of the Joint Genome Institute, a user facility of the US Department of Energy Office of Science. JGI is located at Lawrence Berkeley National Lab in beautiful Berkeley, California.

ALISON : So much thanks to our guests Devaki Bhaya, Michelle Davison, Elisha Wood-Charlson and Dylan Chivian, for sharing their research.

ASHLEIGH : A shout out to the developers of KBase, a team that is spread across multiple labs including: Lawrence Berkeley, Argonne, Brookhaven, and Oak Ridge National Laboratories, as well as Cold Springs Harbor Laboratory, the University of Illinois at Urbana-Champaign, and the University of Tennessee.

ALISON : If you’re interested in trying out KBase, they offer tutorials and webinars, for free! Check ’em out at: k-b-a-s-e dot u-s.

ASHLEIGH : If you enjoyed the podcast and want to help others find us, leave us a review on Apple Podcasts, Google Podcasts, or wherever you like to get your podcasts. If you have a question or want to give us feedback, Tweet us @JGI, or record a voice memo and email us at jgi dash comms at That’s jgi dash c-o-m-m-s at l-b-l dot g-o-v.

ALISON : And because we’re a user facility, if you’re interested in partnering with us, we want to hear from you! We have projects in genome sequencing, synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, algae, and microorganisms. If you want to collaborate, let us know!

ASHLEIGH : Find out more at forward slash user dash programs.

ALISON : And if you want to hear about cutting edge research in secondary metabolites, also known as natural products, then check out JGI’s other podcast, Natural Prodcast. It’s hosted by Dan Udwary and me. That’s it for now. See ya next time!


Phototaxis is the ability of organisms to move directionally in response to a light source. Many cyanobacteria exhibit phototaxis, both towards and away from a light source. In the environment, the ability to move into optimal light conditions for photosynthesis is likely to be an advantage. We are particularly interested in how cells perceive light of different wavelengths the photoreceptors involved and the signal transduction cascade involved in this process.

To dissect the process of motility and phototaxis in Synechocystis sp. we generated a library of transposon-tagged motility-mutants. Several of these tagged-motility mutants mapped to chemotaxis-like genes at loci which we named the tax loci. The roles of chemotaxis proteins in signal transduction are fairly well-understood in flagellated enteric bacteria, but much less so in other systems. Synechocystis sp. has three tax loci, two of which are involved in motility responses. Disruption of the tax1 locus (which contains a photoreceptor, TaxD1) produces mutants that are negatively phototactic while tax3 mutants are non-motile and have no pili. Several novel mutants that are aberrant in phototaxis are being characterized using biochemical and genetic approaches. We have developed a preliminary model of phototaxis and are developing a system to analyze phototaxis in thermophilic cyanobacteria isolated from microbial mats.

We have shown that in the model organism Synechocystis. sp. phototaxis is a surface-dependent phenomenon that requires Type IV pili rather than flagella. Many Gram negative bacteria have Type IV pili, which are long multi-functional, proteinaceous surface appendages. Interestingly, Type IV pili are required for diverse functions such as social motility, host-pathogen recognition, the ability to take up exogenous DNA and in biofilm formation.

Currently we are using time lapse video microscopy and tracking programs to follow single cells and populations to ask basic questions about the parameters that govern motility. In collaboration with Doron Levy (Department of Mathematics, University of Maryland) we are modeling social dynamics in surface dependent motility. We have recently also set up collaborations with K.C. Huang’s group (Department of Bioengineering, Stanford) to simulate and control surface dependent motility. It is likely that cells function as groups and dynamics of group communication may be mediated through pili and molecular signals such as cAMP. The role of communication is particularly relevant to microbial mats and other bacterial communities in natural environments.


RELEVANT PUBLICATIONS (PDF version available under Publications)

Postdoctoral Fellow on Moss-Cyanobacteria Interactions, Sweden

The position is formally located at the department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), in Umeå Sweden. The Post-doctoral Fellow will be jointly supervised by Professors Marie-Charlotte Nilsson Hegethorn and Thomas Moritz, both at SLU Umeå as well as Associated Professor Ulla Rasmussen at Stockholm University. The molecular identification work will be performed at the Swedish Metabolomics Centre, located at the research center Umeå Plant Science Centre (UPSC). UPSC is one of the strongest research environments for experimental plant biology in Europe.

The Post-doctoral Fellow will explore whether and when feather mosses release secondary metabolites to attract and repulse cyanobacterial filaments, and if so, to reveal their chemical identity. The Post-doctoral Fellow will work in a cross-disciplinary research group and carry out laboratory experiments using novel model systems with mosses and cyanobacteria as well as utilize advanced chemical instrumentation in order to characterize moss metabolite(s) underpinning the feather moss and cyanobacteria association. This work will provide advanced understanding of the consequences of moss metabolite profiles for moss-associated communities of cyanobacteria and contribute to a better understanding of the N economy of the moss, and C and N cycling processes in boreal forests that feather mosses drive.

The candidate:

  • should have a PhD degree in biology, biochemistry or in a related field.
  • should have a strong interest in research and be capable of developing the project independently and creatively.
  • It is meriting with experience in chemical analysis, especially chromatography – mass spectrometry techniques.
  • Proficiency in English is required.

As postdoctoral appointments are career-developing positions for junior researchers, we are primarily looking for candidates with a doctoral degree that is three years old at the most.

The application should contain the following written in English: 1) a cover letter describing yourself and your match to the above mentioned project 2) your motivation for the application and 3) your cv and publication list

Cycad Growth form

Cycad plants grow as trees and shrubs. They typically have short trunks topped off with a green crown of large compound leaves. In appearance they closely resemble palm trees, however, they are not closely related.

Most species do not grow more than a few meter tall. Hope’s cycad of Australia is one of the tallest species and is known to reach 20 m (65 ft.) in height. More primitive cycads were often much taller than the majority of cycad species that currently exist.

Stems are usually unbranched and fallen leaves of the past leave leaf scars that encircle the stem. Internally, stems are mostly made up of soft storage tissue rather hard than wood.

The roots of cycads look very unusual and are known as coralloid roots because they have a similar shape to coral. Their roots share an important relationship with the blue-green algae, cyanobacteria. The roots provide the cyanobacteria with protection while the cyanobacteria supplies the roots with nitrogen based nutrients.


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Phytoplankton, a flora of freely floating, often minute organisms that drift with water currents. Like land vegetation, phytoplankton uses carbon dioxide, releases oxygen, and converts minerals to a form animals can use. In fresh water, large numbers of green algae often colour lakes and ponds, and cyanobacteria may affect the taste of drinking water.

Oceanic phytoplankton is the primary food source, directly or indirectly, of nearly all sea organisms. Composed of groups with siliceous skeletons, such as diatoms, dinoflagellates, and coccolithophores, phytoplankton varies seasonally in amount, increasing in spring and fall with favourable light, temperature, and minerals.

Phytoplankton populations in the oceans have been shown to rise and fall according to cycles lasting several years to decades. However, scientists examining records of phytoplankton kept from 1899 to 2008 noted that phytoplankton biomass fell by 1 percent per year in 8 of Earth’s 10 ocean basins, resulting in a cumulative loss of roughly 40 percent. Rising sea surface temperatures over the same period are thought to be the primary cause of this decline.

The Editors of Encyclopaedia Britannica This article was most recently revised and updated by Adam Augustyn, Managing Editor, Reference Content.

We thank Paul Hardy for critical comments on the manuscript.

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Keywords: carboxysome, chloroplast, genetic engineering, photosynthesis, Synechocystis, synthetic biology

Citation: Jensen PE and Leister D (2014) Cyanobacteria as an experimental platform for modifying bacterial and plant photosynthesis. Front. Bioeng. Biotechnol. 2:7. doi: 10.3389/fbioe.2014.00007

Received: 23 March 2014 Accepted: 03 April 2014
Published online: 21 April 2014.

Anne M. Ruffing, Sandia National Laboratories, USA

Anne M. Ruffing, Sandia National Laboratories, USA
Aaron M. Collins, Los Alamos National Laboratory, USA

Copyright: © 2014 Jensen and Leister. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.