MicrobiologyBytes

Cell-cell interactions are common to all living systems. Bacteria are no exception, and numerous mechanisms that use secreted products as signaling molecules are known. Among these, the so-called “quorum sensing” systems are perhaps the best studied. In quorum sensing, all bacterial cells within a population produce secreted molecules. Only when population densities are high is there a response to these compounds, thus allowing the bacteria to coordinate their behavior. However, it is clear that there is much more to bacterial cell–cell interactions than simply counting numbers and coordinating behavior. Secreted molecules also play key roles in microbial development so that different cell fates can arise and coexist within a single-species population. In addition, in settings where multiple species coexist, their interactions often are mediated through extracellular compounds. Development in one microbe can be influenced by small molecules secreted by other species.

Almost all quorum sensing studies have been performed under laboratory conditions – far removed from how bacteria actually live. What happens in the “wild” when rival bacterial gangs contest the same territory?

Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. PNAS USA November 10 2011. doi: 10.1073/pnas.11036301
Many different systems of bacterial interactions have been described. However, relatively few studies have explored how interactions between different microorganisms might influence bacterial development. To explore such interspecies interactions, we focused on Bacillus subtilis, which characteristically develops into matrix-producing cannibals before entering sporulation. We investigated whether organisms from the natural environment of B. subtilis – the soil – were able to alter the development of B. subtilis. To test this possibility, we developed a coculture microcolony screen in which we used fluorescent reporters to identify soil bacteria able to induce matrix production in B. subtilis. Most of the bacteria that influence matrix production in B. subtilis are members of the genus Bacillus, suggesting that such interactions may be predominantly with close relatives. The interactions we observed were mediated via two different mechanisms. One resulted in increased expression of matrix genes via the activation of a sensor histidine kinase, KinD. The second was kinase independent and conceivably functions by altering the relative subpopulations of B. subtilis cell types by preferentially killing noncannibals. These two mechanisms were grouped according to the inducing strain’s relatedness to B. subtilis. Our results suggest that bacteria preferentially alter their development in response to secreted molecules from closely related bacteria and do so using mechanisms that depend on the phylogenetic relatedness of the interacting bacteria.

Tweet

A mycorrhiza is a symbiotic association between a fungus and the roots of a plant. In a mycorrhizal association, the fungus may colonize the roots of a host plant, either intracellularly (arbuscular mycorrhizal fungi) or extracellularly (ectomycorrhizal fungi). These communities are important in plant growth and soil flora. This review focuses on interactions among plants, mycorrhizal fungi, and bacteria, testing the hypothesis whether mycorrhizas can be defined as tripartite associations. After summarizing the main biological features of mycorrhizas, it illustrates the different types of interaction occurring between mycorrhizal fungi and bacteria, from loosely associated microbes to endobacteria. It also discusses, in the context of nutritional strategies, the mechanisms that operate among members of the consortium and that often promote plant growth. Release of active molecules, including volatiles, and physical contact among the partners seem important for the establishment of the bacteria/mycorrhizal fungus/plant network. The potential involvement of quorum sensing and Type III secretion systems is discussed, even if the exact nature of the complex interspecies/interphylum interactions remains unclear.

Plants, mycorrhizal fungi, and bacteria: a network of interactions. Ann Rev Microbiol. 2009 63: 363-83

Related:

• Evolution of root nodule symbiosis with nitrogen-fixing bacteria

Exposure of minerals to rainwater, temperature changes and oxidative conditions results in weathering. All these events have driven the formation of sediments, soils and landscapes, determining soil fertility and water quality. Plants and microbes are also involved in formation and destruction of minerals. For example, microorganisms contribute to precipitation of new minerals and to carbonate production. Whereas carbonate precipitation strongly impacts global carbon cycling – mineral weathering – plays a fundamental role in the environment by influencing the bioavailability of chemical elements that can be either beneficial or toxic to living organisms. Microbial mineral weathering is a widespread key process, not only because of its ecological significance but also because it affects human health, as well as architectural and artistic patrimony. Moreover, bacterial mineral weathering is used by industries to recover scarce metals from ore, and fungi might be useful for bioremediation of asbestos-rich soils. Another exciting possibility is the future use of efficient mineral-weathering bacteria to replace chemical fertilization; these microbes are able to promote the growth of plants by releasing trapped mineral nutrients. This biofertilization might result in a reduction of both economical cost and environmental impact of crop production.

Soil microbes play an essential role in the environment by contributing to the release of key nutrients from primary minerals that are required not only for their own nutrition but also for that of plants. Although the role of fungi in mineral weathering is beginning to be elucidated, the relative impact of bacteria in this process and the molecular mechanisms involved remain poorly understood. This ppaer discusses the ecological relevance of bacterial weathering, mainly in the soil and especially in acidic forest ecosystems, which strongly depend on mineral weathering for their sustainability; molecular mechanisms and genetic determinants involved in the dissolution of complex minerals under aerobic conditions; the potential applications of genomic resources to the study of bacterial weathering.

Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol. Aug 4 2009

Related:

• Soil Bacteria
• Can microbes produce greener sports turf?

PLoS Pathogens is two years old, and to celebrate, they’ve just published a list of the top ten papers downloaded from September 2005 to July 2007, so if you need to catch up on your reading:

1. Carrageenan Is a Potent Inhibitor of Papillomavirus Infection
   Sexually transmitted human papillomavirus (HPV) infections are very common. Although most HPV infections don’t cause noticeable symptoms, persistent infection with some genital HPV types can lead to cervical cancer or other anal/genital cancers. Another subset of HPV types can cause genital warts. Recent studies have suggested that condoms are not highly effective in preventing HPV infection. Although HPV vaccines will soon become available, they probably will not protect against all genital HPV types and will be too expensive for use in the developing world. Inexpensive HPV-inhibitory compounds (known as topical microbicides) might be useful for blocking the spread of HPV. Using a newly developed cell culture–based HPV inhibition test, we have discovered that an inexpensive gelling agent called carrageenan is an unexpectedly potent HPV infection inhibitor. Carrageenan is also under investigation as a topical microbicide targeting HIV and herpes viruses, but it is a thousand times more effective against HPV in cell culture tests. Interestingly, carrageenan is used as a thickener in some commercially available sexual lubricants and lubricated condoms. Several of these commercial lubricant products are potent HPV inhibitors in our cell culture–infection system. Clinical trials are needed to determine the effectiveness of carrageenan as a topical microbicide against HPV.
2. Modulation of Tumor Necrosis Factor by Microbial Pathogens
   In response to invasion by microbial pathogens, host defense mechanisms get activated by both the innate and adaptive arms of the immune responses. TNF (tumor necrosis factor) is a potent proinflammatory cytokine expressed by activated macrophages and lymphocytes that induces diverse cellular responses that can vary from apoptosis to the expression of genes involved in both early inflammatory and acquired immune responses. A wide spectrum of microbes has acquired elegant mechanisms to overcome or deflect the host responses mediated by TNF. For example, modulatory proteins encoded by multiple families of viruses can block TNF and TNF-mediated responses at multiple levels, such as the inhibition of the TNF ligand or its receptors, or by modulating key transduction molecules of the TNF signaling pathway. Bacteria, on the other hand, tend to modify TNF-mediated responses specifically by regulating components of the TNF signaling pathway. Investigation of these diverse strategies employed by viral and bacterial pathogens has significantly advanced our understanding of both host TNF responses and microbial pathogenesis. This review summarizes the diverse microbial strategies to regulate TNF and how such insights into TNF modulation could benefit the treatment of inflammatory or autoimmune diseases.
3. Identification of a Novel Gammaretrovirus in Prostate Tumors of Patients Homozygous for R462Q RNASEL Variant
   Prostate cancer is the most frequent cancer and the second leading cause of cancer deaths in US men over the age of 50. Several genetic factors have been proposed as potential risk factors for the development of prostate cancer, including a viral defense gene called RNASEL. A common genetic variant in this gene, R462Q, was recently implicated in up to 13% of prostate cancer cases. Given the antiviral role of RNASEL, the authors sought to examine if a virus might be present in prostate cancers associated with the R462Q variant. Using a DNA microarray designed to detect all known viral families, the authors identified a novel virus, named XMRV, in a subset of prostate tumor samples. Polymerase chain reaction testing of 86 prostate tumors for the presence of XMRV revealed a strong association between the presence of the virus and being homozygous for the R462Q variant. Cloning and sequencing of the virus showed that XMRV is a close relative of several known xenotropic murine leukemia viruses. This report presents the first documented cases of human infection with a xenotropic retrovirus. Future work will address the potential connection between XMRV infection and the increased prostate cancer risk in patients with the R462Q RNASEL variant.
4. Human Neutrophils Kill Bacillus anthracis
   Bacillus anthracis is the bacterium that causes anthrax, a disease that can occur through natural infections and also through intentional release. B. anthracis makes spores, which are in a dormant state, similar to seeds of a plant, and are extremely resistant to the environment. B. anthracis spores can infect through the skin or the lung. Lung infections disseminate through the body and are lethal. In contrast, skin infections often remain localized, and patients survive even without treatment. It is not well understood why these bacteria cause a localized infection through the skin and a lethal disease through the lung. Little is known about how B. anthracis is controlled. Neutrophils are the first white blood cells recruited to a site of infection and are specialized in killing microbes. Previous studies show that neutrophils are abundant in the skin form, but not in the lung form of anthrax. The researchers report that human neutrophils can take up B. anthracis spores. Once inside, the spores germinate to form vegetative bacteria. The vegetative bacteria are extremely susceptible to neutrophil-killing mechanisms. The B. anthracis virulence factors (molecules that make bacteria cause diseases) manipulate other human cells but do not deter neutrophils. B. anthracis is indeed exquisitely sensitive to the neutrophil protein α-defensin. These data support a new model where B. anthracis skin, but not lung, infections are controlled by the antimicrobial activity of neutrophils.
5. A Novel Bacterium Associated with Lymphadenitis in a Patient with Chronic Granulomatous Disease
   As new bacteria continue to be discovered every year, it is inevitable that some of them will be found to cause human disease. The authors describe the isolation and characterization of a new bacterium, grown from a patient with chronic granulomatous disease (CGD). In this genetic disease, one of the main lines of defense against infection, the neutrophil, has a discrete defect in the generation of superoxide, leading to recurrent infections with a narrow spectrum of bacteria and fungi. This new organism was cultured from lymph nodes that had been inflamed for several months. To prove that this new bacterium was indeed a pathogen, Greenberg and colleagues measured specific antibody response in the patient: they inoculated CGD mice with this organism and reproduced the appearance of the human infection; they recovered the organism in pure growth from infected mouse spleens. This new bacterium belongs to the family Acetobacteraceae, bacteria that are found widely in the environment. They have a variety of industrial uses, such as the production of vinegar, but have never been reported to cause invasive human disease. Disease-causing organisms remain to be discovered. The researchers outline some of the steps that can be taken to verify the pathogenicity of novel organisms.
6. Gene-Specific Countermeasures against Ebola Virus Based on Antisense Phosphorodiamidate Morpholino Oligomers
   Ebola virus (EBOV) causes a highly lethal hemorrhagic fever that results in up to 50%–90% mortality in humans. There are currently no available vaccines or therapeutics to treat EBOV infection. To date, multiple pre- and post-exposure therapeutic strategies, primarily focused on bolstering the host immune response or inhibiting viral replication, have been undertaken with limited success. Here, Bavari and colleagues report the development of a successful therapeutic regimen for EBOV infection based on antisense phosphorodiamidate morpholino oligomers (PMOs). PMOs are a subclass of chemically modified antisense oligonucleotides that interfere with the translation of viral mRNA, thus inhibiting viral amplification. Using a cell-free translation system, a cell-based assay, and survival studies in rodents, we identified several efficacious EBOV-specific PMOs. Further, prophylactic administration of a combination of three EBOV-specific PMOs specifically targeting VP24, VP35, and the viral polymerase L protected rhesus macaques from lethal EBOV infection. This is the first successful antiviral intervention against filoviruses in nonhuman primates. These findings may serve as the basis for a new strategy to quickly develop virus-specific therapies in defense against known, emerging, and genetically engineered bioterrorism threats.
7. The Role of Innate Immune Responses in the Outcome of Interspecies Competition for Colonization of Mucosal Surfaces
   Bacterial infection commonly begins with organisms that colonize and proliferate on mucosal surfaces. These microenvironments may be occupied by multiple microbial species, suggesting that successful colonizers are distinguished by their capacity to prevail over their competitors. This study examines interactions between two bacterial species that both colonize and infect the human upper respiratory tract. In a mouse model, strains of both Haemophilus influenzae and Streptococcus pneumoniae efficiently colonize the nasal mucosa when tested individually. In contrast, following co-inoculation, H. influenzae rapidly and completely outcompetes S. pneumoniae. This competitive effect is dependent on the local responses from the host in the form of a specific type of white blood cell (neutrophil) that acts to engulf and kill microorganisms that have been labeled by proteins that bind to microbial surfaces (complement). The results of this study show that recognition of microbial products from one species may activate inflammatory responses that promote the clearance of another competing species. This study also demonstrates how manipulations such as antibiotics or vaccines, which are meant to diminish the presence of a single pathogen, may inadvertently alter the competitive interactions of complex microbial communities.
8. Prions Adhere to Soil Minerals and Remain Infectious
   Transmissible spongiform encephalopathies (TSEs) are a group of incurable diseases likely caused by a misfolded form of the prion protein (PrP^Sc). TSEs include scrapie in sheep, bovine spongiform encephalopathy (“mad cow” disease) in cattle, chronic wasting disease (CWD) in deer and elk, and Creutzfeldt-Jakob disease in humans. Scrapie and CWD are unique among TSEs because they can be transmitted between animals, and the disease agents appear to persist in environments previously inhabited by infected animals. Soil has been hypothesized to act as a reservoir of infectivity, because PrP^Sc likely enters soil environments through urinary or alimentary shedding and decomposition of infected animals. In this manuscript, the authors test the potential for soil to serve as a reservoir for PrP^Sc and TSE infectivity. They demonstrate that PrP^Sc binds to a variety of soil minerals and to whole soils. They also quantitate the levels of protein binding to three common soil minerals and show that the interaction of PrP^Sc with montmorillonite, a common clay mineral, is remarkably strong. PrP^Sc bound to Mte remained infectious to laboratory animals, suggesting that soil can serve as a reservoir of TSE infectivity.
9. The Expanding Universe of Prion Diseases
   Prions cause fatal and transmissible neurodegenerative disease. These etiological infectious agents are formed in greater part from a misfolded cell-surface protein called PrP^C. Several mammalian species are affected by the diseases, and in the case of “mad cow disease” (BSE) the agent has a tropism for humans, with negative consequences for agribusiness and public health. Unfortunately, the known universe of prion diseases is expanding. At least four novel prion diseases—including human diseases variant Creutzfeldt-Jakob disease (vCJD) and sporadic fatal insomnia (sFI), bovine amyloidotic spongiform encephalopathy (BASE), and Nor98 of sheep—have been identified in the last ten years, and chronic wasting disease (CWD) of North American deer (Odocoileus Specis) and Rocky Mountain elk (Cervus elaphus nelsoni) is undergoing a dramatic spread across North America. While amplification (BSE) and dissemination (CWD, commercial sourcing of cervids from the wild and movement of farmed elk) can be attributed to human activity, the origins of emergent prion diseases cannot always be laid at the door of humankind. Instead, the continued appearance of new outbreaks in the form of “sporadic” disease may be an inevitable outcome in a situation where the replicating pathogen is host-encoded.
10. Crossing the Line: Selection and Evolution of Virulence Traits
    The evolution of pathogens presents a paradox. Pathogenic species are often absolutely dependent on their host species for their propagation through evolutionary time, yet the pathogenic lifestyle requires that the host be damaged during this dependence. It is clear that pathogenic strategies are successful in evolutionary terms because a diverse array of pathogens exists in nature. Pathogens also evolve using a broad range of molecular mechanisms to acquire and modulate existing virulence traits in order to achieve this success. Detailing the benefit of enhanced selection derived through virulence and understanding the mechanisms through which virulence evolves are important to understanding the natural world and both have implications for human health.

Nice work. Open access publishing has come of age.