Fish microbial communities in the Amazon River Basin

New research reveals that fish skin and gut microbiomes respond differently to species and habitat-specific factors, writes Rebecca Borg

South America is home to one of the world’s most diverse river systems globally, with over 3000 freshwater fish species residing in the Amazon River Basin. Its diverse ecosystem comprises various organisms and communities, including several fish species, macroinvertebrates and algae such as macrophytes.

“Having a diverse ecosystem adds to the resilience of freshwater systems,” says aquatic ecologist/ecotoxicologist Dr Aleicia Holland, a Senior Lecturer in Biology, Ecology, Environment & Evolution at La Trobe University. The academic is also the recent recipient of the 2020 Australasia Society of Environmental Toxicology and Chemistry Early Career Medal and the Australian Freshwater Sciences Society Early Career Excellence Award.

While the Amazon Basin thrives from its biodiversity, Dr Holland says that its river system, like many others, finds itself competing against “increasing anthropogenic threats including climate change, urbanisation and deforestation”. Consequently, this places freshwater ecosystems under stress, which Dr Holland says could result in “the loss of different species overtime”.

The Amazon Basin consists of three different types of river systems (black, white and clearwaters), with the primary system, Rio Negro a Blackwater river, deriving its name from the stained black river water which is a result of high dissolved organic matter which lowers pH and makes these systems more acidic. This river, along with Whitewater and Clearwater rivers, was the focus of Dr Holland’s research. She works in collaboration with Biology PhD candidate François-Étienne Sylvain from Laval University in Canada, as well as other researchers from Canada and Brazil.

“The aim of our study was to focus on two elements; to understand the composition of skin and gut microbiomes of Amazonian fish and how this microbiome changes according to different environmental factors,” says Sylvain. “This information is very important because it can be used by stakeholders to better manage habitat exploitation plans affecting these fish.”

Sylvain was funded by National Geographic Society to conduct research on Amazonian fish microbiomes, for which he has also won two awards. His collaborative research paper Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat represents a key milestone in understanding Amazonian fish adaptations.

Skin and gut microbiomes are fundamental in helping fish species adapt to environmental changes that occur within river systems, with both Dr Holland and Sylvain describing it as “essential for a host’s survival”. If a fish doesn’t have a healthy microbiome, they lose a barrier of protection and may be unable to adjust to change.

“Each species of fish has a different microbiome depending on what river system they live in,” says Dr Holland. “It’s important to understand the community composition of fish microbiomes because we need to know what species are out there and how they relate to the genetic diversity of fish species.”

While the main result of the study indicates that microbial communities from different host tissues respond differently to environmental stressors, Sylvain agrees more research is required to understand how microbial communities are subdivided between different body regions, particularly because his study was one of the first to explore the phylogenetic structure of microbiota from different host tissues, and from wild Amazonian fish.

“It raises the question - to what extent do microbial communities from the same host communicate between each other, and how do they mutually influence each other when responding to an environmental stressor?” says Sylvain. “In this regard, future investigations aimed at characterising potential roles of Amazonian fish microbiomes are needed.”