By Dr Kim Handley, University of Auckland
One of the consequences of declining water quality is an increase in cyanobacteria – these are photosynthetic bacteria that live in a wide variety of aquatic or wet habitats.
While they are integral to many aquatic systems, too many cyanobacteria are not a good thing – under favourable conditions cyanobacteria can multiply and form blooms, which can have a serious impact on the environment.
Some cyanobacterial species produce natural toxins, which not only affect river ecosystems and aquatic life, but also threaten human and animal health – thick mats formed by Microcoleus for instance are well known for dog deaths.
What’s more, proliferations of these bacteria are occurring in rivers we consider as having high water quality.
Using genomic technologies to further New Zealand-based knowledge
Genomics is the study of the genome, the complete set of genetic material present in a cell or organism. Environmental genomics research directly samples DNA from the environment, producing partial or full genomes of microorganisms – bacteria, archaea, microeukaryotics and viruses.
The DNA these genomes are generated from is a complex mixture derived from the different microorganisms species (and other organisms) present in a sample. Untangling this mixture requires specialised computational approaches. This type of research can be applied to habitable environments as diverse as soil, your kitchen counter, the human gut, and the ocean.
Genomics Aotearoa has been funding stream to ocean microbiome research in an effort to better understand the links between microbial life in stream, estuary and sea ecosystems.
As part of this approach, a collaboration between the University of Auckland School of Biological Sciences and the Cawthron Institute used genomic and mass spectrometry techniques in a study to identify the genes and proteins present in less well-studied benthic (river or lake bed dwelling) cyanobacteria, such as Microcoleus.
We were especially interested in using these technologies to understand how blooms exist in rivers when levels of the essential nutrient, phosphorus, is very low.
A wealth of useful genomic information was produced from studying Microcoleus mat communities that grew during a 19-day bloom event over a New Zealand summer, the results of which have been published in The ISME Journal: https://www.nature.com/articles/s41396-020-0676-5#Abs1.
Our study shows Microcoleus are equipped with diverse mechanisms for acquiring nitrogen and phosphorus, enabling them to proliferate and out-compete others in low-phosphorus waters, while taking advantage of nitrogen compounds likely introduced by agricultural runoff.
Throughout a proliferation event, Microcoleus species can source nitrogen via urea and nitrate uptake. Interestingly, some source both organic and inorganic forms of phosphorus simultaneously.
Mat on rock from the Wai-iti River
These bacterial species also possess mechanisms for storing carbon, nitrogen and phosphorus in granules within their cells, which they can use when needed for cell growth.
Our study has helped us to see the role these cyanobacteria have alongside the other bacteria and microbial eukaryotes within the New Zealand ecosystem. For instance, Microcoleus rely partly on organic phosphorus scavenged from the wider mat community, while other bacteria, such as Bacteroidetes and Myxococcales species, recycle the biomass from these cyanobacteria or predate on them.
Knowing the various processes used by the cyanobacteria for acquiring nutrients from the mat environment means we better understand how they are able to flourish in low nutrient New Zealand habitats. Understanding the conditions needed for the bacteria to grow and thrive will then potentially help us predict and manage bloom formations, and better manage water quality.
Dr Kim Handley is based at the University of Auckland and leads the Environmental Metagenomics project for Genomics Aotearoa.
Find out more about Environmental Metagenomics here