The Frozen Potential of Microbial Collections

Aug. 16, 2019

If you don’t have a collection at home, you almost certainly know someone who does. Collections range from stamps to fine art to living microbes and can exist as the personal collection of an individual all the way up to national collections. When it comes to their treasures, collectors are equal parts enthusiasts, historians and curators. This curation distinguishes a collector from a hoarder. A collection requires purpose, maintenance and, in a scientific collection, value to the research community. 
Our collections are meant to last, and that intention arises from a sense of stability and conviction that, even beyond a human lifetime, the collection will provide value. This is especially true when an entire field of science bands together to amass and store organisms of collective interest for posterity. Such collections are at once a sign of health and promise for a field, as these collections can enhance reproducibility, provide a window back in time and represent as-yet-unrealized potential. Microbial collections strengthen the field of microbiology and society by extension, so it is important that we get to know and continue to support these collections.

What is a Microbial Collection? 

Microbial collections are curated resources where microbes can be deposited, stored for long periods of time and obtained upon request.  
A scientist at the National Renewable Energies Laboratory removes a stack of boxes containing tubes of cryopreserved algae from a tank cooled by liquid nitrogen.

There are cases to be made that your body is your own personal microbial collection or that each microbiology lab houses focused collections isolated from the environment, borrowed from colleagues or ordered from larger collections. But where would a microbiology lab get their strain library? Dedicated organizations maintain larger microbial collections, with expressed missions to collect, curate and distribute microbes. These are the types of collections that may join larger collecting consortia, like the United States Culture Collection Network
Microbial collections can have both a generalist or a specialist scope for the types of included organisms. The American Type Culture Collection (ATCC), a nonprofit “global bioresource center,” maintains a plethora of prokaryotes, eukaryotic microbes and other bioresources, such as non-microbial cell lines. In contrast, the Fungal Genetics Stock Center (FGSC), is more specialized in scope - you may search this collection if you want to obtain a specific fungal mutant.
Different as these collection foci are, it’s worth noting that many were kindled by our government in their early years. In the above examples, the ATCC resided in the Army Medical Museum for a time “owing to lack of funds” and the FGSC was “funded largely by grants from the National Science Foundation.” As a permanent institution, a government can afford to invest in initiatives that are not initially profitable, but accrue value over time. Microbial collections fall squarely into this category as they become better resources the longer they are maintained.

How are Samples Maintained in Microbial Collections? 

The molecular properties of water create some of the biggest challenges of cryopreservation, or maintaining life in suspended animation at extremely low temperatures. Though its aqueous form is essential to life, its crystalline form (below freezing point) does not play well with living cells. Water crystals result from hydrogen bond expansion, which is bad for cells in the same way that it's bad for a full water-bottle left in the freezer: water expansion can cause cracked outer structures.

How can cells survive the process of cryopreservation? There are natural ways for even multicellular organisms to avoid this cell-popping fate: woolly bear caterpillars famously produce a sort of antifreeze (also called a cryoprotectant) to survive through the winter. Microbial collection centers use cryoprotectants, such as glycerol, to prevent water from forming crystals. Microbes that survive this or other preservation methods, such as freeze-drying, can be processed and stored almost indefinitely. Some microbes, due to their particular biology and inability to survive preservation, are maintained in continuous culture. Both processes require specialized expertise, equipment, and materials, plus a permanent place in an incubator or a freezer.

Why All This Effort to Maintain Microbial Collections?

Julie Russell, head of Culture Collections at Public Health England, described microbial collections as “particularly important because bacteria from the past are vital in helping us understand today’s infectious diseases, develop vaccines and new antibiotics.”

Maintaining thousands of cultures consumes resources and time, not to mention documentation requirements. The major purpose of these collections is to provide scientists a resource where they can deposit and from which they can obtain microbial strains for their studies. Julie Russell, head of Culture Collections at Public Health England, described microbial collections as “particularly important because bacteria from the past are vital in helping us understand today’s infectious diseases, develop vaccines and new antibiotics.” She went on to say that “making the strains available to other scientists allows them to build on discoveries from previous studies, helping to improve human and animal health.” 
These libraries of life provide resources for applications, as illustrated with the USDA Agricultural Research Service Collection of Entomopathogenic Fungi, affectionately called ARSEF (pronounced “ours-F”) by insect pathologists. The USDA maintains these isolates because of the clear value of preserving these fungi to the success of agriculture: insect pathogens provide a service by killing agricultural pests. This collection has been maintained for more than half a century and currently contains over 13,000 isolates of insect-killing fungi. Their catalog keeps track of received isolates over the years and their metadata.
More than a buzzword, this metadata is incredibly useful to researchers in this field. While all microbial collections keep at least enough information to distinguish isolates, relevant information for a collection of insect pathogens includes year of deposition, where the isolate was found, who deposited the isolate, which host insect the pathogen was found to be infecting (when available), and taxonomic classification of the fungus. 
The ARSEF collection allows a scientist to obtain a fungus (Beauveria brongniartii) that killed a citrus long-horned beetle in Japan in 1993 (ARSEF catalog number 6412). This isolate was featured in a study published 15 years later, which tested the ability of 20 fungi to infect the citrus long-horned beetle. These fungi hailed from New York, Illinois, Connecticut, Canada, Austria, China and Japan. Of these fungi, 18 had been deposited in ARSEF, each with a unique history like isolate number 6412.
A long-horned beetle infected with Beuaveria brongniartii.

Today, we could envision sequencing the genome of this fungus, but at the time it was deposited this was not feasible. This is a great strength of such microbial collections, by carefully maintaining these microbes, they open doors to research we can’t even imagine. There is no doubt scientific tools that haven’t been invented will be used on isolates lying in wait in microbial collections right now. 

Frozen foresight

The scientists who deposited the B. brongniartii isolate did so for 2 reasons. First, the onus of maintenance is now on ARSEF, freeing the scientists’ time for research. Second, deposition allows scientists around the world, including the original depositing scientists, to obtain the strain at any point in the future. The valuable fungus and its information is carefully curated by ARSEF. Inclusion in this database also makes the fungus freely available (with appropriate permits) to other insect pathologists, enabling (indirect) collaboration not only with known colleagues, but potential colleagues worldwide.

How did researchers know these repositories would be valuable during the birth of new scientific fields? This decision required profound foresight. A unifying factor in all of their origin stories is room full of dedicated scientists committed to creating a resource not only for themselves, but also for subsequent generations. The ATCC has enjoyed status among the largest collections since its establishment over 100 years ago. It stands as a testament to the decision by microbial collection pioneers in the Society of American Bacteriologists, better known today as the American Society of Microbiology, to invest heavily in the future of microbiology. They did so knowing that this resource would pay dividends for public health and our understanding of the world among us. By learning about and supporting these collections, we can ensure they continue to be valuable resources for generations to come.

Author: Brian Lovett

Brian Lovett
Brian Lovett is a PhD candidate studying mycology in agricultural and vector biology systems.