GOLD Ecosystem Classification paths describe the surroundings from which an environmental sample or an organism is collected. This five-level hierarchical classification system shown below, was originally described by Ivanova et. al. in a paper titled "A call for standardized classification of metagenome projects.“
To facilitate the annotation and classification of a large number of diverse environmental samples and organisms we need a simple, versatile and adaptable classification system. GOLD ecosystem classification provides a simple but powerful framework to describe samples from environmental, host associated as well as engineered or built environments.
This classification system is not a comprehensive list of all possible paths from any given environment, host or engineered setting. Instead it is primarily driven by the samples we curate. Within this framework we periodically review and revise these paths based on existing as well as the new samples we encounter.
The Five Levels of the classification system are as follows.
Ecosystem -> Ecosystem Category -> Ecosystem Type -> Ecosystem Subtype -> Specific Ecosystem
The Ecosystem at the top of this hierarchy describes the broader environment (Environmental, Engineered and Host-associated) from which a sample is collected whereas Specific Ecosystem at the bottom refers to a specific feature within that environment.
Ecosystem: An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively.
Ecosystem Category: Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. For example, the Environmental ecosystem is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc.
Ecosystem Type: Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. For example, the Aquatic ecosystem category may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc.
Ecosystem Subtype: Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. For example, Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category.
Specific Ecosystem: Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. They help to define samples based on very specific characteristics of an environment under the five-level classification system.
Ecosystem Classification Explorer provides an interactive interface to see existing ecosystem classification paths and associated biosamples or organisms.