Plants without bacteria? is it theoretically possible?

I know from school, that all live on the Earth need bacteria as low-level "machines" that break down/extract/convert/produce chemical elements and combinations, other high-level organisms needed. But it is a natural way.

But is it possible to have a world with plants (without mammals or microorganisms and without bacteria) that could exist in the long term. Saying the atmosphere of these world has already enough nitrogen, oxygen and CO2, and of course there is water.

What could break this artificially created world with such conditions (say the world created not from low-level living structures)? Could bacteria emerge in the world?

This is the sort of question that should be considered from more than one perspective. Since this is speculation, take it as a given that there is a lot of 'what if' here.

I doubt most animals and plants can do entirely without bacteria - as you say most of the essential nutrients come from bacteria, who fix nitrogen. If only plants were left on earth, eventually the plants would use up all the nitrogen and they would have to find a way to fix more.

Can bacteria emerge from just a world of plants? I don't think viruses arise spontaneously, but since genomes often have viruses embedded in them, over the course of a billion years or so, its possible since bacteria and viruses continue to be impressed upon our genomes. Would it happen in time? Most would be skeptical whether that timing could work out.

In practice it would be hard to create a world like this. I would be interested to see whether you could sterilize the microorganisms off of seeds without killing the plant for instance. If you're asking about a small sterile environment with only plants, you could do it by adding the nutrients the plants need and giving them sunlight. Such self sustaining systems have been made with cyanobacteria and i'd be surprised if plants could not be included. But these are closed systems and judged by limited amounts of time, so whether this is an answer to your question is not clear. Here it looks like some water plants and fish have been done. If there was a plant that created CO₂ at an adequate rate its possible.

At one time there were no animals at all. Its thought that for a while there might have only been photosynthetic structures that lay in the water and soaked up the rays. Its not clear whether as some say there were colony formations of cyanobacteria as we see today, or whether there may have been larger pre-cellular or proto-cellular structures. But recovering the pre-cambrian configurations of genes from just plant genomes seems like a gambler's bet to me.

Think of it this way: Life always goes uphill, from less developed to more adapted, better at surviving and reproducing.

Early life would be a basic mechanism, trivial in nature, that under the right conditions would kind of replicate itself (kind of, since the replica would be less similar to the original, than when comparing current parent-child similarity). This would basically be a cell. And a cell would remain a cell unless combining with other cells and specializing in functionality would have a certain benefit. Check out this educational video on abiogenesis by cdk007, based on Jack Szostak's work.

But, you know that evolution isn't the process of change of all individuals of a species in a single direction, towards another species. It's a process of forking. So, basic cells of species A could evolve into single cells of species B, but that would only mean the extinction of A if the new environment with the new organisms becomes hostile, if resources are scarce, if species A is less adapted than everyone else, so everyone else occupies A's niche.

Thus, when multicellular organisms evolve, there are A LOT of monocellular organisms already present and occupying important niches. All available sources of energy are being used. If something isn't used - it's a new niche for any accidental mutation that enables the organism to use that niche and prosper as a new species. So anyway you look at it, multicellular organisms won't start existing without single cell organisms surrounding them. So all multicellular organisms will have an environment that includes these "bacteria", so they will adapt to this environment. It's easier to learn to live with something rather than learning to fight with them and then occupy their niche, because the killing and changing to occupy the niche requires much more changes in the organism.

Life on earth is balanced, such as each species occupies its important place in the circulation of substances. This happened not just by chance, but it's the only probable outcome from the process of evolution by natural selection. Having a world that's totally rid of any trace of primitive life forms is next to impossible. On earth we still have species of archaea that are similar to species present on earth billions of years ago. Read this article on Wikipedia aboutNanoarchaeum equitansto get a grasp on the diversity of life.

One of the most important roles played by bacteria is the fixation of nitrogen. Biological nitrogen fixation is carried out primarily by bacteria. There are no known plants that express nitrogenase type enzyme. So plants cannot fix nitrogen.

Without bacteria in the ecology… the ecosystem is in trouble from nitrogen starvation.

That said, denitrification, the removal of fixed nitrogen and conversion back to nitrogen gas is also catalyzed by bacteria. So no bacteria, no lost of nitrogen by biological means.

Nitrogen can be fixed by lightning discharge. About 5%-8% of all nitrogen is fixed this way However lightning does tend to cause forest fires… which results in the lost of nitrogen.

So where does that leave us? We will have to guess how much nitrogen is lost from forest fires (and burial by sedimentation) vs gain from lightning discharge.

That is is not at all easy to guess. In a world of high rainfall (lots of rain forest)… you can have plenty of lightning and no fires. But a world of swamps would have also plenty of organic matter (and nitrogen) being lost through sedimentation. A drier world would have more fires.

If anything… I would guess that such a world is unstable in the long term, certainly on a geological time scale. Eventually the environment will change to one where nitrogen is lost, and fixation by lightning is reduced… and the ecology will collapse from nitrogen starvation.

Could bacteria emerge in the world?

My guess is no. A second abiogenesis event is unlikely to occur when life is already present. The plant alive on your world would prevent any new form of life re-emerging. Plants are not quiet neighbors minding their own business. Plants secrete toxin to poison other plant. Limit growth. (Walnuts are a great example) Plant root do absorb simple sugars and amino acids. Example. So the raw material for new life will not accumulate.

That said… there is no reason why plant life cannot simplify itself to a single cell… such extremes have happened to parasitic barnacles of the Sacculina genus… which look less like a crustacean (ie crab) than barnacles normally do and more like fungus. So we could have single cell plants… descended from higher plants.

What is uncertain is if plants could re-evolve an enzyme to fix nitrogen. Nitrogenase (nif) appears to have evolved once in methanogens and by lateral gene transfer was moved to many other bacteria.

Making food without photosynthesis

by Guest Expert 18 August 2019 18 August 2019

We live in interesting times. The specters of overpopulation and climate change are constantly in the headlines. The possible threat of global food shortages as a result of increased food demand and climate change-induced crop failures is hovering just over the horizon. And we keep hearing the same mantra: we can’t go on producing and consuming food the way we used to. So how can humanity get out of this fix with the minimum amount of societal upheaval and ecological disaster? If we are to fundamentally alter our food production practices, we must start with a bird’s-eye view of the basic biophysical principles of our current food production system. We may need to begin making food without photosynthesis.

Synthetic biology accomplishments

In theory, any novel gene regulatory networks can be assembled from simple genetic components to produce behavior/activities designed by the biologist. However, one of the first productions of a functional gene regulatory network (a ‘toggle-switch’) from simple genetic components required quantitative mathematical modeling ( Gardner et al., 2000 ). A genetic toggle-switch is a synthetic, bistable gene regulatory system. Multiple genetic designs are possible for a genetic toggle-switch for example, Gardner et al. (2000 ) produced such a switch using two repressible promoters arranged in a mutually inhibitory network. A functional toggle-switch required the definition of multiple genetic parameters that were mathematically modeled, and the regulatory network was assembled based on this model. The genetic switch was used to produce or not produce green fluorescent protein (GFP). The expression showed a sharp sigmoidal curve indicating bistability or the ability to exist in two states (in this case with or without GFP production). A key difference between their work and traditional genetic engineering is that they manipulated the network architecture based on theoretical parameters ( Gardner et al., 2000 ). Genetic toggle-switches may have many applications in plant biology, such as precise ‘on switches’ for plant pharmaceutical production, or regulation of biomass accumulation.

Timing is a key aspect of living systems that regulates processes such as circadian rhythms and periodicity. An oscillatory network showing that timing features can be designed synthetically was produced using a series of transcriptional repressors that controlled expression of GFP ( Elowitz & Leibler, 2000 ). To produce the designed periodicity, Elowitz and Leibler developed a mathematical model for transcriptional/translational rates and decay rates of both mRNA and repressor proteins, and the GFP reporter. Understanding the mechanisms behind this artificial oscillatory network could reveal insight into the mechanisms of natural circadian clocks and the development of artificial clocks in living organisms. In plants, such an inducible timing mechanism could be engineered to coordinate flowering time in crop plants.

Remarkably, synthetic biologists have also been able to design systems where programmed multicellular pattern formation was produced ( Basu et al., 2005 ). Natural pattern formation typically involves cell−cell communication that is then interpreted by an intracellular genetic network. Two sets of cells were engineered: ‘sender cells’ that produced a signaling molecule, acyl-homoserine lactone (AHL), and ‘receiver cells’ that produced a fluorescent protein in response to user-defined ranges of the AHL. By varying the spatial arrangement of sender cells and receiver cells, distinct ring-like patterns of GFP fluorescence were produced (Fig. 1). A key to accomplishing the ring pattern was the design of distinct types of receiver cells or ‘band-detect’ strains that had different genetic networks to detect and respond to a high, medium or low AHL concentration. Like previous work, the precise engineering of the genetic circuits used both theoretical and experimental analyses of various parameters (e.g. stability of proteins, strength of promoters). Mathematical models were able to define both individual cell behavior and spatiotemporal multicellular system behavior. In the receiver cells, three fluorescent proteins (GFP red fluorescent protein, RFP cyan fluorescent protein, CYP) were used as the output for the genetic network. From an undifferentiated lawn of receiver cells, a bullseye pattern was produced from CYP, RFP and GFP around a central sender colony ( Basu et al., 2005 ). Synthetic pattern formation may provide quantitative understanding of natural processes, and opens doors to the possibility of engineering three-dimensional tissues ( Basu et al., 2005 ). While pattern formation and its underlying genes have long been studied in plants, synthetic pattern formation could produce application-specific products. For example, by synthetically engineering the ability to control cell division planes, one could envision wood products that have dimensions for specific applications (e.g. a true block of wood rather than a block cut from an elongated tree).

Synthetic pattern formation from multicellular bacterial systems. (a) A schematic illustrating the communication and response between sender and receiver cells. In sender cells, the LuxI gene catalyses synthesis of the acyl-homoserine lactone (AHL) signaling molecule in response to aTc. Sender cells, also producing red fluorescent protein, become sources for the AHL signal. Receiver cells engineered with band-detect networks respond to distinct concentrations of AHL. At high AHL concentrations, green fluorescent protein (GFP) is repressed, at medium AHL concentrations GFP is expressed, and at low AHL concentrations GFP is again repressed to produce ring-like patterns. Different patterns are produced, caused by the arrangement of sender cells on lawns of various band-detect strains. To produce an ellipse (b) two discs of AHL-producing sender cells are used to produce a heart-shaped pattern (c) three discs are used to produce a four-leaf clover shape (d) four discs are used. (a) Modified from Basu et al. (2005 ) (b–d) reproduced from Basu et al. (2005 ) with permission.

Another application of synthetic biology is producing ‘biological machines’, or living organisms designed to perform a specific task. One example is a bacterial camera that was built to produce a chemical image corresponding to an applied light pattern ( Levskaya et al., 2005 ). This biological camera uses a photosensitve phytochrome from cyanobacteria fused to the well characterized two-component signaling system, EnvZ−OmpR. The signaling system controls expression of LacZ that enzymatically produces a black compound in the presence of β-gal-like substrate. This work showed that a simple biological machine can be produced by interfacing different, naturally occurring molecular components.

A synthetic biosensor was produced in bacteria using computationally designed receptors ( Looger et al., 2003 ). To delineate synthetic protein design, the Hellinga laboratory focused their efforts on the evolving zone, the region of ligand-receptor contact, and used periplasmic binding proteins that exhibit a hinge-binding mechanism. The hinge-binding mechanism allowed use of a fluorophore to screen computer-optimized synthetic receptors for functionality. Using these approaches, they demonstrated that a broad range of receptors can be designed: for example, receptors for an explosive, trinitrotoluene (TNT) a sugar, l -lactate a neurotransmitter, serotonin a nerve gas surrogate and the metal zinc have all been designed ( Dwyer et al., 2003 Looger et al., 2003 Allert et al., 2004 ). These receptors were shown to be highly specific, and often detected nanomolar concentrations of their ligands. To demonstrate that these receptors function in vivo, they used a histidine kinase-signaling system with synthetic feedback to reduce background ( Looger et al., 2003 ). In response to nanomolar levels of a specific ligand, a conformational change is induced in the computer-designed receptor. The receptor−ligand complex then develops high affinity for the extracellular domain of transmembrane histidine kinase, activates the histidine kinase, and initiates signal transduction leading to the production of GFP. The system is extremely powerful because the receptors can be computationally designed to most small molecules. Moreover, because the receptors are the first part of the histidine kinase signal transduction system, they provide a modular function. By altering the receptor, bacterial biosensors can be produced to sense molecules such as explosives, chemical agents and environmental pollutants.

Possibility of Silicon-Based Life Grows

Science fiction has long imagined alien worlds inhabited by silicon-based life, such as the rock-eating Horta from the original Star Trek series. Now, scientists have for the first time shown that nature can evolve to incorporate silicon into carbon-based molecules, the building blocks of life on Earth.

Artist rendering of organosilicon-based life. Organosilicon compounds contain carbon-silicon bonds. Recent research from the laboratory of Frances Arnold shows, for the first time, that bacteria can create organosilicon compounds. This does not prove that silicon- or organosilicon-based life is possible, but shows that life could be persuaded to incorporate silicon into its basic components. Credit: Lei Chen and Yan Liang ( for Caltech

As for the implications these findings might have for alien chemistry on distant worlds, “my feeling is that if a human being can coax life to build bonds between silicon and carbon, nature can do it too,” said the study’s senior author Frances Arnold, a chemical engineer at the California Institute of Technology in Pasadena. The scientists detailed their findings recently in the journal Science.

Carbon is the backbone of every known biological molecule. Life on Earth is based on carbon, likely because each carbon atom can form bonds with up to four other atoms simultaneously. This quality makes carbon well-suited to form the long chains of molecules that serve as the basis for life as we know it, such as proteins and DNA.

Still, researchers have long speculated that alien life could have a completely different chemical basis than life on Earth. For example, instead of relying on water as the solvent in which biological molecules operate, perhaps aliens might depend on ammonia or methane. And instead of relying on carbon to create the molecules of life, perhaps aliens could use silicon.

Carbon and silicon are chemically very similar in that silicon atoms can also each form bonds with up to four other atoms simultaneously. Moreover, silicon is one of the most common elements in the Universe. For example, silicon makes up almost 30 percent of the mass of the Earth’s crust, and is roughly 150 times more abundant than carbon in the Earth’s crust.

Scientists have long known that life on Earth is capable of chemically manipulating silicon. For instance, microscopic particles of silicon dioxide called phytoliths can be found in grasses and other plants, and photosynthetic algae known as diatoms incorporate silicon dioxide into their skeletons. However, there are no known natural instances of life on Earth combining silicon and carbon together into molecules.

Still, chemists have artificially synthesized molecules comprised of both silicon and carbon. These organo-silicon compounds are found in a wide range of products, including pharmaceuticals, sealants, caulks, adhesives, paints, herbicides, fungicides, and computer and television screens. Now, scientists have discovered a way to coax biology to chemically bond carbon and silicon together.

“We wanted to see if we could use what biology already does to expand into whole new areas of chemistry that nature has not yet explored,” Arnold said.

The researchers steered microbes into creating molecules never before seen in nature through a strategy known as ‘directed evolution,’ which Arnold pioneered in the early 1990s. Just as farmers have long modified crops and livestock by breeding generations of organisms for the traits they want to appear, so too have scientists bred microbes to create the molecules they desire.

Scientists have used directed evolutionary strategies for years to create household goods such as detergents, and to develop environmentally-friendly ways to make pharmaceuticals, fuels and other industrial products. (Conventional chemical manufacturing processes can require toxic chemicals in contrast, directed evolutionary strategies use living organisms to create molecules and generally avoid chemistry that would prove harmful to life.)

Arnold and her team — synthetic organic chemist Jennifer Kan, bioengineer Russell Lewis, and chemist Kai Chen — focused on enzymes, the proteins that catalyze or accelerate chemical reactions. Their aim was to create enzymes that could generate organo-silicon compounds.

“My laboratory uses evolution to design new enzymes,” Arnold said. “No one really knows how to design them — they are tremendously complicated. But we are learning how to use evolution to make new ones, just as nature does.”

Researchers in Frances Arnold’s lab at Caltech have persuaded living organisms to make chemical bonds not found in nature. The finding may change how medicines and other chemicals are made in the future. Credit: Caltech

First, the researchers started with enzymes they suspected could, in principle, chemically manipulate silicon. Next, they mutated the DNA blueprints of these proteins in more or less random ways and tested the resulting enzymes for the desired trait. The enzymes that performed best were mutated again, and the process was repeated until the scientists reached the results they wanted.

Arnold and her colleagues started with enzymes known as heme proteins, which all have iron at their hearts and are capable of catalyzing a wide variety of reactions. The most widely recognized heme protein is likely hemoglobin, the red pigment that helps blood carry oxygen.

After testing a variety of heme proteins, the scientists concentrated on one from Rhodothermus marinus, a bacterium from hot springs in Iceland. The heme protein in question, known as cytochrome c, normally shuttles electrons to other proteins in the microbe, but Arnold and her colleagues found that it could also generate low levels of organo-silicon compounds.

After analyzing cytochrome c’s structure, the researchers suspected that only a few mutations might greatly enhance the enzyme’s catalytic activity. Indeed, only three rounds of mutations were enough to turn this protein into a catalyst that could generate carbon-silicon bonds more than 15 times more efficiently than the best synthetic techniques currently available. The mutant enzyme could generate at least 20 different organo-silicon compounds, 19 of which were new to science, Arnold said. It remains unknown what applications people might be able to find for these new compounds.

“The biggest surprise from this work is how easy it was to get new functions out of biology, new functions perhaps never selected for in the natural world that are still useful to human beings,” Arnold said. “The biological world always seems poised to innovate.”

In addition to showing that the mutant enzyme could self-generate organo-silicon compounds in a test tube, the scientists also showed that E. coli bacteria, genetically engineered to produce the mutant enzyme within themselves, could also create organo-silicon compounds. This result raises the possibility that microbes somewhere could have naturally evolved the ability to create these molecules.

“In the universe of possibilities that exist for life, we’ve shown that it is a very easy possibility for life as we know it to include silicon in organic molecules,” Arnold said. “And once you can do it somewhere in the Universe, it’s probably being done.”

It remains an open question why life on Earth is based on carbon when silicon is more prevalent in Earth’s crust. Previous research suggests that compared to carbon, silicon can form chemical bonds with fewer kinds of atoms, and it often forms less complex kinds of molecular structures with the atoms that it can interact with. By giving life the ability to create organo-silicon compounds, future research can test why life here or elsewhere may or may not have evolved to incorporate silicon into biological molecules.

In addition to the astrobiology implications, the researchers noted that their work suggests biological processes could generate organo-silicon compounds in ways that are more environmentally friendly and potentially much less expensive than existing methods of synthesizing these molecules. For example, current techniques for creating organo-silicon compounds often require precious metals and toxic solvents.

The mutant enzyme also makes fewer unwanted byproducts. In contrast, existing techniques typically require extra steps to remove undesirable byproducts, adding to the cost of making these molecules.

“I’m talking to several chemical companies right now about potential applications for our work,” Arnold said. “These compounds are hard to make synthetically, so a clean biological route to produce these compounds is very attractive.”

Future research can explore what advantages and disadvantages the ability to create organo-silicon compounds might have for organisms. “By giving this capability to an organism, we might see if there is, or is not, a reason why we don’t stumble across it in the natural world,” Arnold said.

The research was funded by the National Science Foundation, the Caltech Innovation Initiative program, and the Jacobs Institute for Molecular Engineering for Medicine at Caltech.

3 Answers 3

You might consider whether it is possible to ship the plants on their own faster than the bulk of your stuff. We don't know where you are, but there are certainly courier services that specialize in shipping plants around Europe.

How long plants will survive in zero light depends how actively they are growing. Plants don't just use light for photosynthesis - there are other types of photoreceptor cells which control the plant's metabolism. A dormant cactus or succulent which hasn't been watered at all for a month or two probably won't be affected at all by a week or two in the dark. A fast growing plant which is just about to start flowering is a very different situation.

For an extended period, a small amount of light may be worse than none at all, since the plant may start to make etiolated growth in the direction of whatever light is available.

Fighting Microbes with Microbes

Amy Coombs
Jan 1, 2013

CAPSULE © JORG GREUEL/GETTY IMAGES BACTERIA © JEZPERKLAUZEN/ISTOCKPHOTO.COM L ike humans, with their complement of microbes that aid in everything from immune responses to nutrition, plants rely on a vast array of bacteria and fungi for health and defense. Over the last decade, research has revealed many new functional aspects of the crosstalk between human-associated microbes and human cells, but plant biologists are only beginning to scratch the surface of the often surprising ways that soil microbiota impact plants, from underground fungus-wired alarm systems to soil bacteria that can trigger defensive plant behavior or even act as a sort of vaccine. But despite these benefits, microbes are still primarily thought of as harbingers of disease.

&ldquoSince the discovery of antibiotics, medical research has been dominated by a &lsquobazooka mentality,&rsquo&rdquo and so has agricultural research, says Alexandre Jousset, a plant scientist at the Georg-August University in Göttingen, Germany. &ldquoTraditionally, microbes have.

While the Human Microbiome Project has discovered that some 10,000 species of microorganisms live in and on the human body, outnumbering our own cells by ten to one, plant scientists have found that any given soil sample contains more than 30,000 taxonomic varieties of microbes. Soil microflora not only provide nutrients for plants, but also suppress disease. In exchange, roots secrete fixed carbon into the soil and feed their bacterial symbionts.

Plant scientists have found that any given soil sample
contains more than 30,000 taxonomic varieties of microbes.

Although the medical community now warns that overprescribing antibiotics kills beneficial organisms and encourages the formation of resistant strains, a similar change in opinion has not occurred in agriculture, where a kill-all approach to plant pathogens has given rise to biocides that indiscriminately wipe out the beneficial along with the pathogenic. “Biocides can nuke the soil, but they never kill everything,” says Mike Cohen, a biologist at Sonoma State University in California. “This creates a biological vacuum that becomes filled by opportunistic survivors and organisms from the surrounding soil.” Biocides create a strong selective pressure: the few pathogens that survive face little competition and proliferate, giving rise to pathogenic communities that can evade standard treatments.

Beneficial soil organisms, however, can protect plants more selectively than biocides do. They displace pathogens and produce toxins that kill pathogenic microbes, and they also trigger plants’ own defense mechanisms. “Native bacteria are the first and most powerful barrier to prevent the establishment of pathogens,” says Jousset. “A diverse community is especially important to keeping pathogens away—this is true in the human gut and in the soil.”

“The idea is that we can reduce pesticide and fungicide use by utilizing the microbiome,” says Harsh Bais, a plant biologist at the University of Delaware in Newark. “But we need to know more about the mechanisms of action relationships between microbes and plants are very complex.”

Life Underground

According to a recent study published in PLOS One, underground networks of fungi help tomato plants “eavesdrop” on the alarm signals produced by their neighbors. 1 Even when plants are not able to communicate with chemical cues released through their leaves, they can link up and share vital information under the soil.

Researchers at South China Agricultural University in Guangzhou inoculated tomato plant leaves with the early blight fungus Alternaria solani, which creates brown and dead patches on leaves and can rot the tomato fruit. They then covered all research plants with airtight plastic bags, which prevented the transmission of airborne signals. Despite being covered, the tomato plants were able to communicate. Uninoculated plants growing several feet away activated defense-related genes and started making disease-fighting enzymes.

Researchers traced communication back to the fungus Glomus mosseae, which forms a symbiotic relationship with plant root hair known as a mycorrhizal network by inserting itself into the root cell’s membrane. Bagged tomato plants grown in soil that lacked this underground network were unable to receive the “activate-defenses!” signal from infected neighbors and did not produce disease-fighting compounds. In contrast, in soils containing Glomus mosseae, uninfected plants detected the warning signs of disease and produced higher levels of six defense-related enzymes, including peroxidase (POD), polyphenol oxidase (PPO), chitinase, β-1,3-glucanase, phenylalanine ammonia-lyase (PAL), and lipoxygenase (LOX). (See diagram below.)

Because the mycorrhizal network can extend from one set of plant roots to another, it’s possible that the network of fungal mycelia acts like telephone wires, allowing the plants to communicate underground. If this hypothesis is proven by identifying compounds that relay the chemical signal through the fungi, it might be possible to prevent plant disease by cultivating an appropriate mix of microbes in the soil. “The problem is that we don’t know how plants and microbes select one another,” says Bais.

To try to answer that question, Bais and his colleagues turned to Arabidopsis thaliana plants and Bacillus subtilis, a bacterium known to improve plant health. Despite the plant’s antimicrobial defenses, B. subtilis somehow becomes established in the soil. The team found that B. subtilis secretes an antimicrobial peptide that temporarily suppresses toxins secreted by the root, allowing the beneficial bacterium to colonize the soil around the roots. 2 The peptide secreted by B. subtilis may also help ward off soil-borne pathogens while the plant’s defenses are compromised, says Bais.

Even after a bacterial community wanes, the biochemical pathways developed by the plants in response to bacterial colonization remain intact.

In a prior study, Bais and his colleagues found that plants can pick and choose the beneficial bacteria species recruited during pathogen attacks. 3 The team infected Arabidopsis seedlings with the bacterium Pseudomonas syringae pv. tomato, which causes bacterial speck—a major disease of tomato crops. Plant roots soon began secreting L-malic acid, a food source for B. subtilis. As a result, B. subtilis colonized the roots, which in turn triggered production of the plant’s defense chemical salicylic acid, helping it fight the bacterial infection. “This isn’t a typical symbiotic relationship,” Bais says, “but there is an interesting reciprocity here.” (See diagram below.)

Plants may even be able to recruit different bacterial species as their need for food and water changes. Researchers from Ain Shams University in Cairo, Egypt, recently dissected the root systems of drought-sensitive pepper plants (Capsicum annuum) grown with varying amounts of water. 4 After comparing the structure and diversity of bacterial communities in the rhizosphere, the team found that plants grown in the desert with little water have larger populations of plant growth–promoting (PGB) bacteria which can enhance photosynthesis and biomass synthesis by as much as 40 percent under drought stress. Although PGB’s mechanism of action has not been worked out, the bacteria are known to alleviate salt stress by reducing the production of ethylene in tomato seedlings.

Surprisingly, there is some evidence that the effects of beneficial bacteria can endure across generations. Even after a bacterial community wanes, the biochemical pathways developed by the plants in response to bacterial colonization remain intact. “This suggests the bacteria function as a vaccine of sorts,” says Bais. This heightened disease response can then be passed to the next generation of plants. For example, even when progeny are not exposed to B. subtilis, they are better able to fight disease if parent plants fostered a relationship with the bacterium. “The bacteria help prime the plant to respond more quickly to disease, and they pass this memory to the next generation,” says Bais. The effects appear to last the duration of the offspring plant’s life, but are not passed on to a third generation.

A look at the soil microbiome View full size JPG | PDF © CATHERINE DELPHIA Although most microorganisms that are beneficial to plants reside in the soil, their effects are not always localized to the roots. In a third study, published in The Plant Journal, 5 Bais and his colleagues showed that beneficial soil microbes encourage the closure of stomatal pores in the leaves of Arabidopsis plants. Stomata allow carbon dioxide to diffuse into the leaf and release expired oxygen and water into the air. Hot and dry conditions are known to trigger stomatal closure to preserve a plant’s water, but Bais was the first to show that soil bacteria can trigger the response—an important finding, as some pathogenic bacteria, such as P. syringae pv. tomato, enter the plant through the stomata.

To see if root microbes could help counteract already established plant infections, Bais and his colleagues grew plants infested with P. syringae and then inoculated the soil with the beneficial B. subtilis. As the roots recruited new colonies of B. subtilis, the plants began producing abscisic acid—a chemical known to regulate stomatal closure. After three hours, only 43 percent of stomata were open in B. subtilis-treated plants. In control groups, 56 percent of stomata remained open. “This difference was significant and helped reduce disease,” says Bais.

Unearthing the mechanism of action

It’s much harder for pathogens to take over the human gut when beneficial microflora coat its surface. A similar mechanism is at play in the soil. When it comes to preventing plant disease, some microbes kill pathogens directly others consume resources, taking up the niches that invading bacteria might otherwise inhabit.

“When a community is composed of species that use distinct resources, there is less free room for invading species,” says Jousset. He and his colleagues set out to determine whether a broader genetic diversity of beneficial bacterial strains was more important than simply cultivating a large variety of bacteria, regardless of their genetic makeup.

We might be able to encourage disease-fighting bacterial communities by selecting for the right number and combination of species. —­Alexandre Jousset, Georg-August University,
Göttingen, Germany

The researchers grew 95 microbial communities, each containing between one and eight strains of Pseudomonas fluorescens bacteria—another species known to improve plant health. Each group had varying degrees of genetic similarity. The team then exposed the colonies to the invading bacterial species Serratia liquefaciens, which colonizes soil, water, and even the human gut and urinary tract, where pathogenic strains cause infection. After 36 hours, S. liquefaciens was able to invade communities that contained genetically similar species, but it was not able to gain a foothold in more genetically diverse communities. Indeed, as genotypic dissimilarity increased threefold, researchers saw a linear decrease in the colonization by S. liquefaciens. 6

However, the number of beneficial species in the soil was nearly as important as the degree of genetic dissimilarity between them. Communities with four to six species were better able to ward off invasion. Interestingly, communities were more susceptible to invasion by S. liquefaciens when a lower or higher number of bacterial species was present. Most likely, says Jousset, this is due to the variety of toxins produced. The colonies containing too many species produced a large amount of toxins, some of which also harmed beneficial strains of bacteria, whereas communities with too few species had low levels of toxin production, thus making invasion more likely.

RAPSEED FLOWER © KNAUPE/ISTOCKPHOTO.COM “This suggests we might be able to encourage disease-fighting bacterial communities by selecting for the right number and combination of species,” says Jousset. Like the gut, the soil is an open system that allows bacteria to come and go, and competition for food and nutrients determines community structure. By manipulating food sources and growing conditions in the soil, it may be possible to select for genetically diverse communities. In a recent field study, Jousset sampled the disease-fighting genes found in the soil and discovered that a diverse mixture of planted herbs and grasses gives rise to the best ratio of disease-fighting genes and helps suppress soil-born pathogens. (See “Down and Dirty,” The Scientist, September 2012.)

Creating healthy soil

Just as antibiotics indiscriminately kill both good and bad bacteria in the gut, fungicides and biocides impede the soil’s innate defenses. Studies have shown that gentler practices such as crop rotation, tillage, and fertilization can influence ecological processes in the soil, and may encourage the establishment of microbial communities capable of suppressing disease.

In search of a way to supplement the soil that encourages the growth of beneficial bacteria, Mike Cohen of Sonoma State University joined colleagues at the US Department of Agriculture to test rapeseed (Brassica napus) meal—a waste product from processing rapeseed into cooking oil or biodiesel.

The researchers split the roots of an apple tree seedling so that the plant had roots potted in two different containers. They then introduced the pathogen Rhizoctonia solani, which causes root rot, into one container. Rapeseed meal was incorporated into the soil of the other container at about 0.5 percent of the total volume, whereas the soil inoculated with the pathogen was left untreated. “This allowed us to test the indirect impacts of seed meal on the plant,” says Cohen. 7

The rapeseed meal reduced root rot by about 50 percent relative to control groups grown without the treatment. In fact, the researchers observed that the entire plant benefited from the rapeseed meal even though only half of the roots were exposed. Cohen and colleagues think that rapeseed meal fosters colonization by species of beneficial Streptomyces, known to trigger systemic defenses in plants. There were 10 times as many Streptomyces bacteria in soils amended by rapeseed meal, a finding that was later corroborated by field trials.

THE GOOD STREP: Streptomyces sp. growing on agar for antibiotic research © CHARLOTTE RAYMOND/SCIENCE SOURCE Indeed, when the researchers directly inoculated the split-root soil with Streptomyces instead of rapeseed meal, they found that Streptomyces encouraged plant defenses much as the seed meal did. “We can’t say for sure how Streptomyces benefit the plant,” says Cohen, “but some evidence indicates it’s related to induction of the jasmonic acid signaling pathway,” a hormonal signaling system that triggers plant defenses. (See “How Plants Feel,” The Scientist, December 2012.)

Unfortunately, seed meal can also nourish pathogenic organisms. In some studies, disease-causing microbes proliferated in soils treated with seed meal. However, combining seed meals from mustard, rapeseed, and other plants can help minimize the growth of pathogenic microbes, says Cohen. This is because seed meals contain glucosinolates—chemicals that release pathogen-killing fumigants as they break down in water. As the chemicals released by rapeseed may be slightly different than those of mustard seed,“seed meals are more promising when used in combination,” says Cohen. “One seed meal might target a pathogen, while another will help build beneficial communities of Streptomyces.”

As gastroenterologists are now reporting the efficacy of transplanting gut bacteria from healthy individuals into human patients suffering from intestinal inflammation and infection, plant researchers may also find that multiple treatments with different concoctions of beneficial microorganisms will have a great impact on soil ecology. Even if one species doesn’t curtail a pathogen, a full remake of the microbial community might help kick the problem. The goal is to gradually build the soil over time to establish a favorable microbial ecosystem. In rich, healthy soil, the microbial community may be more resistant to disease.

Researchers are now turning to field experiments to test the best combinations of species, and treatments like seed meal are already being used on organic farms in Northern California. If greater microbial diversity improves plant health in large-scale field trials, it could eventually help reduce chemical loads on industrial farms. “It might not work exactly the same way in the gut, but the mechanisms in the soil are very similar,” says Jousset. “If we can protect and cultivate the soil microbiome rather than kill important species, we might need fewer chemicals in the field.” 

Amy Coombs is a science writer based in Chicago.


1. Y.Y. Song et al., “Interplant communication of tomato plants through underground common mycorrhizal networks,” PLOS ONE, 5(10): e13324, 2010.

2. V. Lakshmannan et al., “Microbe-associated molecular patterns (MAMPs)-triggered root responses mediate beneficial rhizobacterial recruitment in Arabidopsis,” Plant Physiol, 160:1642-61, 2012.

3. T. Rudrappa et al., “Root-secreted malic acid recruits beneficial soil bacteria,” Plant Physiol, 148:1547-56, 2008.

4. R. Marasco et al., “A drought resistance-promoting microbiome is selected by root system under desert farming,” PLOS ONE, 7(10): e48479, 2012.

5. A.S. Kumar et al., “Rhizobacteria Bacillus subtilis restricts foliar pathogen entry through stomata,” Plant J, 72:694–706, 2012.

6. A. Jousset et al., “Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities,” ISME J, 5:1108–14, 2011.

8 Answers 8

If you allow the third kingdom (after plants and animals), namely fungi (mushrooms and their many, many cousins), then yes.

Fungi will take care of the oxygen surplus, using it up and releasing CO2 for the plants to breathe.

For pollenation: There are plants that use the wind for this, and other plants reproduce through non-sexual reproduction - strawberry offshoots, old willow trees breaking apart and new ones growing from the parts, root networks sprouting new aboveground plant parts, potatos and onions creating tubers or child-bulbs underground.

Fertilization: See fungi. Plants die, Fungi (and bacteria) break apart the plant matter, rinse and repeat.

Animals actually take care of only a relatively small part of the "Plant matter to fertilizer and CO2" conversion, with fungi already doing the bulk of the work. Without our contribution to pollination and spread of seeds etc., we could actually consider us animals superfluous for the ecology as a whole )

Edit: Found a book (trilogy) I was thinking of when writing this answer - "Of man and manta", from Piers Anthony. Sci-Fi, features a planet with no animal life where fungi evolved into mobile, and IIRC sapient, beings.

Plants existed before animals ever evolved, and if all animals were to disappear, plants would continue to exist a million years from now. Just mostly different species.

Respiration. Plants produce both CO2 and O2. Without animals, there would be a higher concentration of O2. If you wanted, you could easily evolve plants that have internal processes that take in environmental oxygen at a higher rate than they use CO2, and perhaps use it to increase mobility and growth. Otherwise, it's likely that bacteria would take up any slack, assuming you just didn't re-evolve animals (Oxygen is a great energy source, if it doesn't kill you first).

Pollination. Insects and other animals are only one mechanism by which plants are pollinated. Wind dispersal is an older method, and one that most pine trees use effectively. The plants that cause most spring allergies rely on wind distribution of their pollen.

Soil fertility. In a compost pile, worms are famous for doing the work of breaking waste vegetation into new soil. But this happens even without animals. Instead, soil bacteria and fungus do the job. I wouldn't even suggest that the process needs to slow down.

Seed dispersal. There are lots of plants that rely on animals carrying their seeds, either as food (eaten or stored) or by burrs attached to fur, feathers, or skin. But there are many, many plants that rely on other strategies. Fluffy feathery seeds floating in the wind are common and maple trees with their helicopter seeds are two examples. Seeds in flood areas can use flooding both as a means of being carried away from their parent, and as a signal that it's time to germinate. More unusually, there are even plants whose seed pods explode (video), propelling the seeds many feet away.

Competition and predation. With or without animals, plants need to defend against predation and competition. Dodder and mistletoe are both parasitic plants that get their energy by tapping into the sap of host plants. They don't usually kill the host, but they can certainly weaken it. Strangler figs are a species that germinate on a host tree, then as they grow, they wrap around and choke the host to death. Oak leaves (and others) contain tannins that poison the soil at the tree base, making it harder for other plants to grow there. It's a violent world out there.

If you also eliminated fungi, many, many plants would struggle because they rely on fungus at their roots to increase their nutrient uptake. Without that, plants would probably be limited in size, and many existing species would die.

Microbes Gone Missing

In the early 20th century, biologists began to uncover fascinating relationships between complex organisms and their microbes: in tubeworms that had no mouth, anus or gut in termites that fed on tough, woody plants in cows whose grassy diet significantly lacked protein. Such observations generated excitement and prompted follow-up experiments. In those years, the absence of microbial helpers in an animal wasn’t considered particularly surprising or interesting, and it often received little more than a passing nod in the literature. Even when it was thought to merit more than that — as in a 1978 report in Science that tiny wood-eating crustaceans, unlike termites, had no stable population of gut bacteria — it ended up flying under the radar.

And so expectations quietly began to shift to a new norm, that every animal had a relationship with bacteria without which it would perish. A few voices protested this oversimplification: As early as 1953, Paul Buchner, one of the founders of symbiosis research, wrote with exasperation about the notion that obligate, fixed and functional symbioses were universal. “Again and again there have been authors who insist that endosymbiosis is an elementary principle of all organisms,” he seethed. But counterexamples drowned in the flood of studies on the importance of host-microbe symbioses, especially those that drew connections between human health and our own microbiome.

“The human microbiome has completely driven a lot of our thinking about how microbes work,” said Tobin Hammer, a postdoctoral researcher in ecology and evolutionary biology at the University of Texas, Austin. “And we often project from ourselves outwards.”

But the human example is not a good model for what’s going on in a diverse range of species, from caterpillars and butterflies to sawflies and shrimp, to some birds and bats (and perhaps even some pandas). In these animals, the microbes are sparser, more transient or unpredictable — and they don’t necessarily contribute much, if anything, to their host. “The story is more complex,” said Sarah Hird, an evolutionary biologist and microbial ecologist at the University of Connecticut, “more fuzzy.”

A transient, almost nonexistent relationship with bacteria was what Sanders saw in his tropical ants. He brought his samples back to his lab (then at Harvard University, although he is now at Cornell), where he sequenced the insects’ bacterial DNA and quantified how many microbes were present. The ant species with dense, specialized microbiomes had approximately 10,000 times more bacteria in their guts than Sanders found in the many other species he had captured. Put another way, Sanders said, if the ants were scaled to human size, some would carry a pound of microbes within them (similar to what humans harbor), others a mere coffee bean’s worth. “It’s really a profound difference.”

That difference, reported in Integrative & Comparative Biology in 2017, seemed to be associated with diet: Strictly herbivorous tree-dwelling ants were more likely to have an abundant microbiome, perhaps to make up for their protein-deficient diet omnivorous and carnivorous ground-dwelling ants consumed more balanced meals and had negligible amounts of bacteria in their gut. Still, this pattern was inconsistent. Some of the herbivorous ants also lacked a microbiome. And the ants that did have one didn’t seem to have widespread, predictable associations with particular species of bacteria (although some sets of microbes were common to individual genera of the insects). That result marked a clear departure from mammalian microbiomes like our own, which tend to be very specific to their hosts.

The reasons why would become clearer as case studies of other organisms started to trickle in.

Functional Microbial Diversity

24.2.1 Phylogenetic Position of “Ca. C. subterraneum” Among Archaea

To confirm the phylogenetic position of the thermophile “ Ca. C. subterraneum” among Archaea, we conducted a genome-wide phylogenetic analysis using the maximum-likelihood method with the LG+G substitution model ( Tamura et al., 2013 ). We used a concatenated alignment of 22 broadly conserved proteins among 79 Archaea, including “Ca. C. subterraneum,” and two representative bacterial species (Escherichia coli and Bacillus subtilis) as an out-group. The phylogenetic tree demonstrated that “Ca. C. subterraneum” formed a cluster with five species within Thaumarchaeota ( Fig. 24.1 ) ( Takami et al., 2012a ). The thermophile “Candidatus Nitrospaera gargensis” (“Ca. N. gargensis”) ( Torre et al., 2008 Spang et al., 2012 ) was somewhat distantly related to other mesophilic thaumarchaeotic species species within the families Nitrosopumilaceae and Cenoarchaeaceae comprised a subcluster. Thus, “Ca. C. subterraneum” was closely related to the thermophile “Ca. N. gargensis” based on this phylogenetic tree ( Fig. 24.1 ).

Figure 24.1 . Phylogenetic position of “Ca. Caldiachaeum subterraneum” based on concatenated common protein sequences. A maximum-likelihood tree was constructed using MEGA. The phylogenetic trees were collapsed at the family level except for Nanoarchaeum, “Candidatus Korarchaeum,” and “Candidatus Caldiarchaeum.” A concatenated alignment of the sequences of 22 common proteins with no paralogs and no domain splitting (hisS, pheS, valS, rpl11p, rpl14p, rpl1P, rpl22p, rpl2p, rpl3p, rpl5p, rpl6p, rplW, rps10p, rps11p, rps19p, rps2P, rps3p, rps4p, rps5p, rps7p, rps8p, and rps9p) among 142 archaea, including “Candidatus Acetothermus autotrophicum,” and two bacteria as an out-group were used for phylogenetic analysis. The numbers shown along branches indicate the bootstrap support expressed as percentages.

What is the relevance of the GM crop debate to ecologists?

We have serious problems with the application of GM technologies, not only because many people have serious emotional reservations, but also because our understanding of the environment and how it functions is so limited. We are seeing dramatic declines in many species of farmland bird and wild plant species, which we know to be associated with changes in farming practice over the last few decades but find very difficult to tie down to specific agricultural practices ( Fuller et al. 1995 ). For example, autumn sowing of crops is certainly important in restricting the food available for some bird species, and the use of agrochemicals is also important ( Fuller et al. 1995 ). However, even for such well-documented organisms as birds, direct cause and effect relationships are difficult to understand in detail. The position is very much worse with plants and invertebrates, as there have been far fewer long-term surveys that enable correlations of declines with specific agricultural practices ( Donald 1998 ). As a result, when the release of herbicide-tolerant or insect-resistant crops is contemplated there is a real problem in deciding if such crops will further enhance declines in the species that are affected. Weed control is a direct elimination of biodiversity within fields, as well as a major reduction in food for wildlife. Likewise, if all crops are resistant to insects what will birds in the future eat? Controls of weeds and insect pests are an integral part of agricultural practice, whether it is intensive or organic. Intensive agriculture is a greater problem because such controls are more efficient, reflecting five decades of agricultural policy to enhance food production. Therefore, is there a logical reason why GM crops bred to reduce pest problems should be discriminated against? It is clearly unreasonable but surely it is not unreasonable to strive to reduce the impact of pest control on wildlife, whether the methods involve GM crops or not?

In the UK we have the problem that many of the species of plants and animals we want to conserve are the products of previous agricultural practice, so that any change in farming leads to changes in wildlife. In the absence of human management, wildlife would be dominated by the plants and animals best adapted to living in forests. Our concerns about GM crops need to change from an overemphasis on the slight risk that crops and genes may move from farmers’ fields into our few remaining areas of uncultivated land, to a proper recognition of the dramatic impact that changes in agricultural policy can have on our landscapes. GM crops can be produced and managed in ways that are less environmentally harmful than present crops they can also be bred and used in ways that will enhance existing declines in wildlife. The challenge for ecologists is to be able to provide clear advice on the changes in farming practice that are needed to produce the environment we want. The challenge for politicians is to determine what people really want from our environment and how much they are willing to pay farmers to provide it for them. The challenge for all of us is to decide which plants and animals we want, and how many there should be of each species.

I believe that the only effective way to manage farms to produce more biodiversity will be through a system in which the yield of wildlife has a commercial value to the farmer. Only then will the selection of seed, management practices and the desire to enhance wildlife be driven by those with the greatest ability to ensure that the changes we desire are achieved. I have no doubts that many, perhaps most, farmers would wish to be able to enhance the environmental quality of their farms, but are heavily constrained from doing so by the need to generate adequate incomes under the constraints of the Common Agricultural Policy. We should no more expect farmers to produce more flowers in their fields without remuneration than we should expect city dwellers to provide flowering window boxes without financial incentives.

A window of opportunity has opened up for ecologists to produce the research needed for us to understand better how agriculture can produce the biodiversity we want, and to facilitate risk assessments for the introduction of new crops, whether they be GM or not. Resolution of the first problem will certainly not be solved by an idealistically driven move to widespread organic farming birds starve whether fields are ploughed in the autumn by intensive or organic farmers. Neither will it be resolved by the blind use of technology. Statements of intent to produce more biodiversity and greater numbers of individual species are meaningless unless linked to realistic means to achieve the goals. Once we have a clear picture of the agriculture we want in the future it will be much easier to judge GM or traditionally bred crops for their environmental benefits and disadvantages. It will also be much easier for breeders to develop crops that are best suited for an agriculture that is being managed to satisfy environmental needs.

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