1. As the Planet Gets Hotter…. Microbes Can Increase Drought Tolerance in Plants

Drought is a significant source of abiotic stress that impacts plant growth and crop production. The threat of warming soil temperatures and a changing climate have only intensified these concerns, but microbes can help! A number of studies have implicated bacteria in the drought resistance of plants, and a couple of recent papers provide thought-provoking data that should catalyze future experimentation on the subject. Scientists are exploring ways to enhance the natural ability of plant-growth-promoting bacteria (PGPB) to alleviate drought stress in plants through the solubilization of mineral nutrients in the soil; production of important chemicals that help regulate plant growth, called phytohormones; and the production of osmolytes, molecules that maintain cell integrity by regulating the viscosity, melting point and ionic strength of biological fluids.

Plants in Morocco suffering from drought.One study, published in the Chemical Engineering Journal, demonstrated that an engineered strain of obligate methanotroph, Methylotuvimicrobium alcaliphilum 20Z, could overproduce the phytohormone indole 3-acetic acid (IAA) from methane. The new strain was able to convert a dangerous greenhouse gas to a usable plant-growth-promoting hormone at high titers, and researchers further proved that microbial treatment of wheat seeds with the IAA-producing strain under saline-alkaline conditions caused markedly increased germination and elongation of the shoots and roots of the plant. The authors proposed a promising approach to simultaneously reducing greenhouse gas emissions and facilitating sustainable crop production, suggesting that the strategy should be expanded as a seed treatment biofertilizer.

Other studies have been looking at strategies to assess drought tolerance in agricultural lands. A study published in mSystems used stable isotopes and Raman spectroscopy to quantify microbial phenotypes of drought-tolerant bacteria in soil samples and found that (depending on the sample) 0%-52.2% of all measured single cells exhibited drought-tolerant properties. Furthermore, scientists were able to relate the phenotypic properties of the soil microbiome to the behavior of surrounding plants under drought conditions. In other words, soil samples that were rich in drought-tolerant bacteria were correlated with heartier plants. Metagenomic analysis helped link these phenotypic properties to genes that encode phytohormone production.

2. And the Planet’s Water Gets Hotter…. Microbes Are Migrating to New Environments as a Result of Warming Temperatures

Many pathogenic microbes have adapted a thermotolerance that allows them to thrive at host body temperatures, and studies indicate that warming climates may select for, and allow, pathogenic microbes to inhabit new environments that were previously considered less–than hospitable. Nigleria fowleri, also known as the brain-eating ameba, has been detected as far north as the upper-Midwest in the U.S., and scientists think warming temperatures may be to blame. N. fowleri is free-living and thermophilic in nature. The ameba is commonly found in warm fresh water and soil, preferring high temperatures of up to 45°C. Although infection is rare, it is a particularly dangerous pathogen due to its ability to cross the blood/brain barrier and cause acute brain infection upon nasal passage entry, known as primary amebic meningoencephalitis (PAM), which is typically fatal within 3-7 days of symptom onset. A Centers for Disease Control and Prevention Emerging Infectious Diseases dispatch analyzed trends in recreational water exposure associated with PAM cases in the U.S. from 1978-2018, and noted air temperature increases (compared with 20-year historic averages) in the 2 weeks prior to PAM exposures in the Midwest. The observation led researchers to suggest that warming temperatures, along with increased recreational water usage, may be contributing to the observed northward expansion of PAM cases.

Vibrio and warming temps. Other dangerous pathogens belonging to the Vibrio genus have been increasing in prevalence in marine environments. It has previously been determined that slight increases in water temperature can have a dramatic effect on Vibrio colonization, prompting scientists to recently study sea-surface temperature data around the English and Welsh coastlines in an attempt to identify locations where conditions for the presence and growth of Vibrio species is favorable. The research is published in Water Research. Researchers collected shellfish from 3 separate locations that were experiencing sea-surface temperature increases and detected Vibrio species in samples from all 3 locations. Some of the specific species that were identified (i.e., Vibrio rotiferianus and Vibrio jasicida) had not previously been reported in U.K. waters. The study suggests that the increased biodiversity and prevalence of Vibrio species may be tied to warming water temperatures and decreased salinity caused by heavy summer rainfalls.

3. Why Microbes Cause Earthy Odors After a Rainstorm

A drop of dew on a fallen leaf.You might be surprised to learn that it is microbes, not earthworms, that produce the earthy smell that fills the air after a good rainstorm. The source, geosmin, is a naturally produced chemical compound that is heavily conserved in actinobacteria, myxobacteria, cyanobacteria and some fungi. Although the odorous terpene is detectible at picomolar concentrations by humans, its biological function remained elusive until the recent publication of a study in Applied and Environmental Microbiology. In this study, researchers hypothesized, and were able to demonstrate, that geosmin is used as a warning signal by toxin-producing microbes to ward off eukaryotic predators. The addition of the chemical to agar plates containing Caenorhabditis elegans, a free-living nematode that feeds on bacterial species, repelled the worms, even in the absence of bacteria. Furthermore, a predation assay revealed that geosmin reduced C. elegans grazing on Streptomyces coelicolor bacteria. While geosmin itself was not harmful to the worms, the bacteria produced a number of toxic metabolites that were up-regulated when bacterial sporulation was triggered by grazing. Geosmin was therefore shown to benefit both predator and prey.

4. Historic Shipwrecks Form Islands of Microbial Biodiversity on the Seabed

Fish swim through a sunken ship.Sunken ships introduce man-made structures and materials that are unnatural to marine environments. However, over time, and with significant help from microbes, these abandoned vessels become artificial reefs teeming with life. Now researchers are investigating how wooden shipwrecks influence the biodiversity and ecology of deep-sea sediment microbiomes. In a study published in Limnology and Oceanography, scientists used 16S rRNA gene amplicon sequencing to identify microbes in samples taken from 2 different deep-sea wooden shipwreck sites. The wreckage was located at water depths of 525 m and 1800 m, respectively, and samples were collected along 60 m transects extending in 4 directions from the hull of each boat. This particular experimental design allowed researchers to consider distance from the shipwreck and depth of the sediment as potential factors contributing to microbial diversity and abundance.

Sequencing revealed that the composition of the sediment microbiome was distinct and consistent across shipwreck sites, and researchers were able to identify unique habitat patches on the ocean floor that resembled those that have been associated with organic tree falls. Increased diversity of anaerobic archaea, including Bathyarchaeia and Lokiarchaeia, was detected at the deeper shipwreck site, as was a higher abundance of Bacteroidetes, Chloroflexi, Desulfofarculales and Desulfobacteriales bacteria. Samples taken nearer the shipwreck revealed more unique taxa, including microbes that can break down complex organic matter, metabolize cellulose and fix sulfur. It is still unknown whether these microbes were introduced to the sea floor by the shipwreck or they were already present and enabled to thrive when new raw materials were introduced to the ecosystem. However, scientists have concluded that shipwrecks may serve as especially significant sources of organic matter in oligotrophic areas that are far from shore and otherwise offer low levels of nutrients.

5. Conserved Bacteria Found in Human Breast Cancer Cells May Contribute to Metastasis

A microscopic 3D view of tumor cells.Microbes have been found living inside the tumor cells of a variety of cancer types. However, until recently, little was known about the functional significance of resident microbiota. A recent study published in Cell used a murine spontaneous breast-tumor model MMTV-PyMT to better understand the role of microbes in tumor growth and/or metastasis. While depletion of intracellular bacteria did not affect primary growth of the tumor, it did significantly reduce the development of secondary malignant growths. Scientists further determined that the bacteria actually promoted the survival of tumor cells during metastatic colonization by reorganizing the actin cytoskeleton to be more resistant to fluid sheer stress. Introduction of select bacteria strains in two murine tumor models generated similar results, suggesting that tumor-resident bacteria stimulate metastasis and are therefore an important consideration in cancer treatment and care.

6. Microbes Are Key Drivers of Honeybee and Vulture Bee Health 

The gut microbiome is comprised of microbial communities that reside in the digestive tract and are critical to the health and development of host species. Although the gut microbiota of adult bees is highly conserved, diet, stress, physical activity, exposure to pathogens and age have all been shown to influence microbiome function and composition. While the vast majority of bees feed on pollen and nectar, vulture bees, a small, stingless group that inhabits tropical rainforests, demonstrate a necrophagous lifestyle. These bees collect and feed on carrion, the decaying flesh of dead animals. The role of microbes in this extreme dietary shift remains undefined and of great interest. Therefore, an mBio study sought to better understand the microbial implications of a necrophagous diet. Scientists used deep sequencing, 16S rRNA genomic sequencing and community analyses to compare the microbiomes of vulture bees and closely related species that are consumers of both meat and pollen (facultatively necrophagous), as well as those that consume only pollen (obligate pollinivorous). Data revealed that the vulture bees had lost some core microbes, retained others and had notably gained an abundance of novel acidophiles, which were present in both the environment and on carrion food sources of the bees. Because acidophilic bacteria have also been found in other animals that feed on carrion, scientists hypothesized that an acidic gut is likely important for digestion and nutrition under necrophagous diets.

Vulture bees The gut microbiome of adult honeybees, one of the most well-characterized of all animals, is similarly conserved and adapted to dietary requirements. For example, honeybees have been shown to harbor bacteria that facilitate the digestion of toxic sugars found in the nectar of some plants. However, less is known about bacteriophage communities in bee digestive systems. In a recently published mSystems paper, scientists sequenced the virome of western honeybees obtained in Austin, Texas. Sequencing results were compared to the viromes of 2 European bee populations, which were previously characterized.

Thirteen phage clusters were shared amongst European and U.S. bees. However, most of the bacteriophages associated with the bees collected in the U.S. were novel, leading researchers to suggest that the phages coevolved with their bacterial hosts. Neither study quantified bacterial abundance, and hosts for 25-50% of phages, including 1 of the 13 conserved species, could not be identified. Therefore, much about these host-microbe dynamics remains to be explored. This was the first time widespread geographic variation in bacteriophage composition was considered for honeybee populations.

7. New Insights into Antimicrobial Resistance

What do we know about the afterlife of dead bacteria? A recent Applied and Environmental Microbiology study found that dead cells can transfer antibiotic resistance genes to live bacteria via horizontal gene transfer. Researchers tracked the movement of extracellular antibiotic resistance genes (eARGs) from dead antibiotic-resistant Pseudomonas stutzeri cells to live P. stutzeri in antibiotic-free soil, even at low concentrations, and demonstrated that natural transformation from dead bacteria can contribute to the spread of antibiotic resistance, even in the absence of antibiotic selection.

New insights in AMR
Researchers are further investigating examples of indirect AMR selection, including the long-term use of atypical antipsychotic (AAP) medication. AAPs target dopamine and serotonin receptors and are used to treat symptoms of psychiatric disorders. However, demonstration of intrinsic antimicrobial activity has prompted concerns about the development of antimicrobial-resistant bacteria as an unintended consequence of long-term AAP treatment. Scientists recently published a study in the Journal of Bacteriology that demonstrated that Escherichia coli isolates demonstrated increased minimal inhibitory concentrations for ampicillin, tetracycline, ceftriaxone and levofloxacin after 6 weeks of exposure to an AAP called quetiapine at gut concentrations. Whole genome sequencing identified a number of mutations in genes that are linked to AMR, revealing an important connection between AAP use and AMR in E. coli.

For more about AMR and countering misconceptions in the field, check out research published in the Journal of Microbiology and Biology Education, in which researchers developed a set of reading interventions and an assessment tool to confront intuitive misconceptions leading students to misconceive antibiotic resistance as a goal-oriented process of evolution, as opposed to the accrual of random genetic variations that allow some bacteria to survive, reproduce and form resilient populations. The study provides insights to the understanding of AMR by undergraduates and has clear implications for promoting a better understanding of AMR by the general public.

8. Dog Behavior Is a Key Factor in the Transmission of Rabies Infections

A caged rabid dog.Scientists sought to characterize the transmission dynamics allowing rabies virus to continue circulating at low levels, despite control efforts, in Tanzanian dog populations. From 2002-2016, researchers traced rabies transmission in a population of 50,000 dogs in Tanzania. The data, published in Science, was spatially resolved, allowing modeling to be applied to individual dog behaviors. It was discovered that while some dogs simply bite other animals in their surrounding environments, others travel long distances and introduce new virus lineages to neighboring populations. This dispersal can lead to cocirculation of lineages and metapopulation persistence. Overall, this study indicated that individual dog behavior is a key determinant of rabies transmission dynamics, and the authors argue that the findings may have important implications for other pathogens that circulate in spatially structured populations.

Author: Ashley Hagen, M.S.

Ashley Hagen, M.S.
Ashley Hagen, M.S. is the scientific and digital editor for the American Society for Microbiology and host of ASM's Microbial Minutes.

Author: Stanley Maloy

Stanley Maloy
Stanley Maloy is a professor of microbiology and associate vice president for innovation at San Diego State University.