The Stream Microbiome: An Ecosystem’s Health Report Card

Image Credit: mstk east, CC BY 2.0, Image Cropped

Thanks to DNA sequencing, there is no escape from the reality that every organism is an ecosystem. I like to think of myself as an individual human organism but actually, I am a holobiont, playing host to thousands of other species. Back in college, my body was an ecosystem in distress. A diet of coffee, beer, and bagels coupled with a steady dip of stress led to a series of health issues and an eventual diagnosis of ‘dysbiosis’. Dysbiosis is a term that describes a loss of microbial biodiversity or departure from a balanced ecology.

A microscopic community of organisms associated with a particular habitat and set of environmental conditions is called the ‘microbiome’. The term ‘microbiome’ was originally coined by Whipps and colleagues in 1988 and it has since been widely applied in human health research. The human microbiome includes bacteria, archaea, fungi, protozoans, and by some definitions, viruses. The distinct microclimates and resources throughout our bodies harbour distinct communities of microorganisms. The gut microbiome gets most of the press but there is a skin microbiome, a nasal microbiome, and even an armpit microbiome. We share microbes with the people we encounter and the environments we inhabit. 

The human microbiome includes an array of bacteria, seen here thanks to the National Human Genome Research Institute (Clockwise from top left): Streptococcus (Credit: Tom Schmidt); microbial biofilm of mixed species, from human body (Credit: A. Earl, Broad Institute/MIT); Bacillus (Credit: Tom Schmidt); Malassezia lopophilis (Credit: J.H. Carr, CDC). Credit for composite image: Jonathan Bailey, NHGRI. CC BY-NC 2.0

Now that DNA sequencing is becoming less expensive, the characterization of microbiomes is extending out from the human body into more traditional ecosystems.  

In my PhD research, I explored the stream microbiome. In a stream, the microbiome includes the same microscopic players as in the human body but joined by photosynthetic algae. Just as the human gut, skin, and mouth harbor distinct microbiomes, there are different components of the stream microbiome in the water, sediment, and the slimy biofilm that coats submerged surfaces. The stream microbiome provides a snapshot of the factors shaping the stream ecosystem. 

It is also worth noting that DNA collected from a stream ecosystem not only describes the microscopic community, it can also be used to monitor larger organisms. DNA collected from water, air, or soil samples is dubbed environmental or ‘eDNA’. When vertebrates such as fish, frogs, and mammals leave scales, poop, skin cells, and/or fur in their wake, they are depositing DNA in their environment. In aquatic ecosystems, the water becomes a repository for all of this genetic material. As a result, the presence of rare or invasive species can be determined from a water sample, no sighting or catching required. Lots of research in underway to determine the persistence of DNA from various parts of various critters across various ecosystems. Currently, different assays are required to consider macro and microfauna but in the future, it may be possible to inventory all the organisms within an environmental sample using a single tool.   

The stream microbiome could eventually serve as a stream health report card that reflects environmental conditions but first, healthy and unhealthy microbiomes must be characterised and differentiated. In humans, a universal definition of a ‘healthy microbiome’ has been elusive due to the broad diversity across individuals and populations. Instead, it has been easier to link a particular disease to an out-of-whack microbial community through a diagnosis of dysbiosis. This approach is now being employed in ecosystems. For example, marine biologists have linked dysbiosis to the susceptibility of corals to disease and bleaching events. The microbiome provides a helpful diagnostic tool because disease and death often occur due to the combined effects of multiple stressors rather than from a single impact or pathogen.

In freshwater ecosystems, dysbiosis has been considered within certain fish and shellfish species but has not been generally applied to the stream environment. Attributing ecological dysbiosis to specific environmental stressors could eventually provide a valuable tool in locating and diagnosing sources of impairment. For instance, microbial demographics may signal the presence of elevated nutrients or heavy metals. Microbial community patterns are also important because the ability of microorganisms to effectively metabolize inputs and produce nutritious outputs is equally relevant in our bodies and our waterways. 

The slimy biofilm that coats the submerged surfaces in a stream is one compartment of the stream microbiome. (Image credit: Krista Bonfantine, CC BY-SA 2.0)

Even if we can detect the cause of impairment in streams, the next step is mitigating the impact. In some cases, ecological impairment may be improved by reducing the input of a pollutant. In my case, a reduced supply of coffee and beer helped to treat the dysbiosis and probiotic supplements helped to restore the ecological balance of my gut microbiome. I’m lucky those treatments worked because in some cases, patients require a fecal transplant to reintroduce good gut microbes. In stream ecosystems, poop sharing is less cringey but the concept is still relevant. Each member of the ecosystem has a role in maintaining and sharing the microbes that keep the system in balance. In the past, we’ve considered fish species as predators and prey. We haven’t thought much about the poo perspective but perhaps we should? Researchers have found that fish feces interact with elevated temperatures to produce coral dysbiosis.

Although the microbiome concept introduces a mind-blowing level of complexity to every organism and ecosystem, it also hints at a system of checks and balances that is constantly shifting to support the web of life. Rather than be dismayed by the complexity, I am inspired by the inherent diversity and self-healing properties and I can’t wait to see what science will teach us about the similarities between our internal and external ecosystems.


Krista Bonfantine is a PhD student at Deakin University studying the effectiveness of environmental flows using DNA metabarcoding and citizen science. Her background includes water and fire management and her passion is connecting science and society for a better, wetter world. You can read more of her work at her Ecology for the Masses profile, learn more about her on her website or follow her on Twitter.

One comment

  • Enjoyed your article. Interesting to apply microbiome to the stream environment or any environment….and to use as a litmus of ecosystem health. The gut of a single person can be massively complex. Boggles the mind to consider the complexity of an entire river microbiome. Best to you.

    Liked by 1 person

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