Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, 53706, USA.
Annual Review of Microbiology (Impact Factor: 12.18). 07/2008; 62(1):375-401. DOI: 10.1146/annurev.micro.030608.101423
Source: PubMed


Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.

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Available from: Kenneth F. Raffa
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    • "There are experimental data indicating that competitive interactions are predominant among microbial species[6,43,44]. Nevertheless, other studies that have documented positive interactions among microbial species [e.g.,[45]] lead to conclusion that positive interactions are dominant in microbial communities. In this study, the positive interaction between Serratia marcescens and Candida rugosa under environmental stress was reflected in elevated growth rates of both organisms when cocultured at subinhibitory phenol concentrations . "
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    ABSTRACT: There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation.
    Full-text · Article · Jan 2016 · The Scientific World Journal
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    • "Microbial populations influence each other during the development of their ecosystems, while at the same time the microbial ecosystem is affected by its surrounding environments and vice versa (Fernández et al., 2000; Hashsham et al., 2000; Little et al., 2008; Klitgord and Segrè, 2010). It is predicted that the sustainability of an ecosystem will be maintained by dynamic changes of the bacterial community (dynamic equilibrium) (Ishii et al., 2012; Yamamoto et al., 2014). "
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    ABSTRACT: This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and "interspecies interaction," were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, "interspecies interaction," a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.
    Full-text · Article · Nov 2015 · Frontiers in Microbiology
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    • "A more recent method is biotization, or the introduction of beneficial bacteria to tissue culture plants (Sturz and Nowak, 2000). By using a community of bacteria rather than one strain, the community is more stable and robust to perturbations , and synergistic responses have been observed on plant growth (Jessup et al., 2004; Bhattacharjee et al., 2008; Little et al., 2008). "
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    ABSTRACT: Soil bacteria have the ability to increase agricultural sustainability through the production of biopesticides and biofertilizers. Application of bacteria to field crops often results in sporadic colonization and unpredictable crop performance. This research sought to understand the colonization of the potato (Solanum tuberosum L.) rhizosphere using reciprocal transplants. Plants were grown in a forest or an agricultural soil and then transplanted into either the same soil or the opposite soil. Bacterial communities were profiled using terminal restriction fragment length polymorphism (TRFLP) and analyzed using pairwise comparisons. The results revealed that the bacterial community that colonized the rhizosphere in the first soil remained mostly intact for 30 days after the plants were transplanted into another soil in which the soil bacteria community differed from that found in the original soil. The concept that it may be possible to establish a functional microbiota and to deliver it to an agricultural environment was tested. A nitrogen-fixing bacterial community was established on plants grown under tissue culture conditions and the plants were transplanted into a field soil. Plants inoculated with eight separate nitrogen-fixing communities showed an average fivefold increase in dry biomass when compared to mock-inoculated plants and the microbial profiles remained distinct at 30 days after transplantation. These results demonstrate that the plant rhizosphere is a resistant community and that the first bacterial community that becomes established on the root remains with the plant even when the plant is placed into soil with a vastly different microbiota.
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