Captured Diversity in a Culture Collection: Case Study of the Geographic and Habitat Distributions of Environmental Isolates Held at the American Type Culture Collection

The use of molecular techniques to assess prokaryotic diversity independent of the need for enrichment culture has profoundly changed how we view and study microbial diversity. As molecular data have accumulated over the past 15 years, these data are now resulting in a healthy debate about how much we really know about prokaryotic diversity in a wide range of environments (8, 21–23, 32, 44, 55). A number of recent articles have discussed these questions, and opinions range from the position that prokaryotic diversity is essentially infinite, with the existence of millions of potential species, (6, 10), to arguments that microbial diversity is reasonably finite (17, 26). In light of this debate concerning the results of theoretical considerations and molecule-based surveys, it is interesting to take stock of the holdings of the environmental prokaryotes available at the American Type Culture Collection (ATCC) to determine how these holdings reflect overall trends in microbial diversity in different habitats. The principle mission of bioresource centers, such as the ATCC, is to serve as living stock collections that acquire diverse biological materials for redistribution to researchers throughout the world. The ATCC has about two-thirds of the type strains of prokaryotic species in the world. In many cases, multiple strains of a given species are acquired. As these materials are accessioned, data relevant to their provenance and physiology are collected. These data are an underutilized asset of bioresource centers. For example, the data on the source locations of isolates can provide information about the relative sampling efforts for different geographic regions. Concordantly, data concerning the environmental habitats of isolates can provide important information about the diversity of genera that are associated with certain habitat types. No articles were found in a literature search that specifically analyzed culture collections as a metric for assessing our knowledge of larger patterns of microbial diversity. In this article we present an analysis of the holdings of environmental prokaryotes at the ATCC with regard to the geographical and environmental habitats from which they were isolated. The term environmental is broadly defined to include all organisms that are not pathogenic to humans or animals or that are not otherwise human associated (see below). Selected habitats for which holdings at the ATCC are the most abundant were compared to recently published findings of workers who used cultivation-independent methods to assess microbial diversity. This provided perspective on how well the “captured diversity” in a culture collection represents the diversity which may exist in nature.