Читать книгу Clinical Guide to Fish Medicine - Группа авторов - Страница 102

Aquatic systems are rich in microbes, including bacteria, archaea, protists, fungi, and microalgae such as diatoms. This microbiota is found within the water column and attached to all surfaces. On wet surfaces, this microbiota creates a sheltered scaffold known as the biofilm. Assessment of this microbiome in aquarium systems is in its infancy, including the relationship to fish health and biological filtration.

Bacterial indicator tests use selective bacterial media designed to look for point sources of human fecal contamination in surface water. Various commercial tests are available (e.g. total coliforms and fecal coliforms on Colilert, or Enterococcus spp. on Enterolert, both by Idexx, Westbrook, ME). In‐house testing relies on either membrane filtration or multiple‐tube fermentation methods with results available one to two days later as number of colony‐forming units (CFU)/100 mL for membrane filtration and most probable number (MPN)/100 mL for multiple‐tube fermentation; these results are equivalent. In the United States, targets are often extrapolated from state or US‐EPA regulations for swimming beaches or USDA regulations for marine mammal habitats. These tests likely have value when assessing open systems with human access where point contamination with human sewage is possible (e.g. swim with ray programs in outdoor lagoons). However, these bacterial indicator tests are problematic in most fish systems because of a high risk of false positives (e.g. growth of plant‐based Enterococcus spp. or nonselected genera such as Vibrio spp.) and because they may not have any relation to pathogen load (Pisciotta et al. 2002; Culpepper et al. 2016). Rather than a measure of potential fish morbidity, these tests may be most useful in determining if disinfection needs have changed over time: once a baseline has been established for the system, higher values may suggest a change in bacterial load in that system. However, the tests only represent a very small proportion of the total microbiome.

A more complete view is possible using fluorescent microscopy. This can directly determine populations of micro‐organisms, including a wider variety of bacteria as well as viruses. To determine the types of micro‐organisms, DNA analysis is required (microbiomics). This involves extracting, amplifying, and sequencing genomic DNA. Microbiome analyses have been reported for closed aquarium systems and have shown changes in bacterial diversity and evenness following routine maintenance such as water changes (Van Bonn et al. 2015; Patin et al. 2018). Further information and resources are available at the Aquarium Microbiome Project (www.aquariummicrobiomeproject.org).