Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking

Abstract

Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.

Evolutionary limits to cooperation in microbial communities

“…This view contrasts with empirical surveys of natural bacterial communities, which suggest that competitive interactions predominate over cooperative interactions (31). However, it has also been suggested that cooperation between different genotypes may explain the unculturability of many species in the laboratory when in monoculture (32)(33)(34). If correct, studies with culturable species could underestimate cooperativity in microbial communities.…”

Black Queen evolution: the role of leakiness in structuring microbial communities

“…Beneficiary microbes dependent on diffusible products produced by helpers appear to be very widespread in nature. For instance, most microcolonies from a soil community developed more quickly when other community members were growing nearby [9]. Many previously unculturable bacteria have been induced to grow in the laboratory using coculture either with mixed natural communities [10] or with specific helper microbes [6,8,11].…”

ColTapp, an automated image analysis application for efficient microbial colony growth dynamics quantification

“…Additionally, it can report metrics characterizing color, 72 shape and proximity of neighboring colonies. We speculate that ColTapp will prove useful in a broad 73 spectrum of microbiology applications, such as species identification in environmental samples as 74 shown by Ernebjerg & Kishony (2012). 75…”