Rules of engagement: interspecies interactions that regulate microbial communities

Interspecies chemical communication in bacterial development

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Rhizosphere chemical dialogues: plant-microbe interactions

Every organism on earth relies on associations with its neighbors to sustain life. For example, plants form associations with neighboring plants, microflora, and microfauna, while humans maintain symbiotic associations with intestinal microbial flora, which is indispensable for nutrient assimilation and development of the innate immune system. Most of these associations are facilitated by chemical cues exchanged between the host and the symbionts. In the rhizosphere, which includes plant roots and the surrounding area of soil influenced by the roots, plants exude chemicals to effectively communicate with their neighboring soil organisms. Here we review the current literature pertaining to the chemical communication that exists between plants and microorganisms and the biological processes they sustain.

What is microbial community ecology?

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Quorum-sensing control of antibiotic synthesis in Burkholderia thailandensis

The genome of Burkholderia thailandensis codes for several LuxR-LuxI quorum-sensing systems. We used B. thailandensis quorum-sensing deletion mutants and recombinant Escherichia coli to determine the nature of the signals produced by one of the systems, BtaR2-BtaI2, and to show that this system controls genes required for the synthesis of an antibiotic. BtaI2 is an acyl-homoserine lactone (acyl-HSL) synthase that produces two hydroxylated acyl-HSLs, N-3-hydroxy-decanoyl-HSL (3OHC(10)-HSL) and N-3-hydroxy-octanoyl-HSL (3OHC(8)-HSL). The btaI2 gene is positively regulated by BtaR2 in response to either 3OHC(10)-HSL or 3OHC(8)-HSL. The btaR2-btaI2 genes are located within clusters of genes with annotations that suggest they are involved in the synthesis of polyketide or peptide antibiotics. Stationary-phase cultures of wild-type B. thailandensis, but not a btaR2 mutant or a strain deficient in acyl-HSL synthesis, produced an antibiotic effective against gram-positive bacteria. Two of the putative antibiotic synthesis gene clusters require BtaR2 and either 3OHC(10)-HSL or 3OHC(8)-HSL for activation. This represents another example where antibiotic synthesis is controlled by quorum sensing, and it has implications for the evolutionary divergence of B. thailandensis and its close relatives Burkholderia pseudomallei and Burkholderia mallei.

Patterns and scales in gastrointestinal microbial ecology

The body surfaces of humans and other animals are colonized at birth by microorganisms. The majority of microbial residents on the human body exist within gastrointestinal (GI) tract communities, where they contribute to many aspects of host biology and pathobiology. Recent technological advances have expanded our ability to perceive the membership and physiologic traits of microbial communities along the GI tract. To translate this information into a mechanistic and practical understanding of host-microbe and microbe-microbe relationships, it is necessary to recast our conceptualization of the GI tract and its resident microbial communities in ecological terms. This review depicts GI microbial ecology in the context of 2 fundamental ecological concepts: (1) the patterns of biodiversity within the GI tract and (2) the scales of time, space, and environment within which we perceive those patterns. We show how this conceptual framework can be used to integrate our existing knowledge and identify important open questions in GI microbial ecology.

Fabrication of microbial biofilm arrays by geometric control of cell adhesion

This paper presents a technique for patterning arrays of microbial biofilms on a wide range of different substrates using thin polymer stencils. The stencils function as "scaffolds" that provide geometric control over cell adhesion on surfaces and confine biofilm growth to specific regions of a substrate. We demonstrate the fabrication of biofilm arrays with features (e.g., individual biofilms) as small as 50 microm in diameter with physiological characteristics that are reproducible. Biofilm arrays of a range of microorganisms can be produced using this technique, including: P. aeruginosa, B. subtilis, S. epidermidis, V. fischeri, E. coli, and C. albicans. This approach provides a simple, user-configurable, and relatively inexpensive method for growing biofilms in both static and flow conditions. The method described in this paper makes it possible to study the chemical, physical, and environmental factors that affect biofilm development in a statistically relevant and reproducible format.

Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation

Shifts in microbial communities are implicated in the pathogenesis of a number of gastrointestinal diseases, but we have limited understanding of the mechanisms that lead to altered community structures. One difficulty with studying these mechanisms in human subjects is the inherent baseline variability of the microbiota in different individuals. In an effort to overcome this baseline variability, we employed a mouse model to control the host genotype, diet, and other possible influences on the microbiota. This allowed us to determine whether the indigenous microbiota in such mice had a stable baseline community structure and whether this community exhibited a consistent response following antibiotic administration. We employed a tag-sequencing strategy targeting the V6 hypervariable region of the bacterial small-subunit (16S) rRNA combined with massively parallel sequencing to determine the community structure of the gut microbiota. Inbred mice in a controlled environment harbored a reproducible baseline community that was significantly impacted by antibiotic administration. The ability of the gut microbial community to recover to baseline following the cessation of antibiotic administration differed according to the antibiotic regimen administered. Severe antibiotic pressure resulted in reproducible, long-lasting alterations in the gut microbial community, including a decrease in overall diversity. The finding of stereotypic responses of the indigenous microbiota to ecologic stress suggests that a better understanding of the factors that govern community structure could lead to strategies for the intentional manipulation of this ecosystem so as to preserve or restore a healthy microbiota.

Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans

Symbiosis is receiving increased attention among all aspects of biology because of the unifying themes it helps construct across ecological, evolutionary, developmental, semiochemical, and pest management theory. Insects show a vast array of symbiotic relationships with a wide diversity of microorganisms. These relationships may confer a variety of benefits to the host (macrosymbiont), such as direct or indirect nutrition, ability to counter the defenses of plant or animal hosts, protection from natural enemies, improved development and reproduction, and communication. Benefits to the microsymbiont (including a broad range of fungi, bacteria, mites, nematodes, etc.) often include transport, protection from antagonists, and protection from environmental extremes. Symbiotic relationships may be mutualistic, commensal, competitive, or parasitic. In many cases, individual relationships may include both beneficial and detrimental effects to each partner during various phases of their life histories or as environmental conditions change. The outcomes of insect-microbial interactions are often strongly mediated by other symbionts and by features of the external and internal environment. These outcomes can also have important effects on human well being and environmental quality, by affecting agriculture, human health, natural resources, and the impacts of invasive species. We argue that, for many systems, our understanding of symbiotic relationships will advance most rapidly where context dependency and multipartite membership are integrated into existing conceptual frameworks. Furthermore, the contribution of entomological studies to overall symbiosis theory will be greatest where preoccupation with strict definitions and artificial boundaries is minimized, and integration of emerging molecular and quantitative techniques is maximized. We highlight symbiotic relations involving bark beetles to illustrate examples of the above trends.