By Genomics Aotearoa 13/07/2020 2


Dr Kim Handley, University of Auckland

Just how do cyanobacteria live in their natural habitat, and how do they coexist with other bacteria and microbial life forms?

And what difference will knowledge on this bacteria have on maintaining New Zealand’s water quality?

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.

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.


2 Responses to “Better understanding bacterial blooms in New Zealand waterways”

  • As an occasional swimmer in the Wai-iti River where this field work was carried out, I’ve noticed that the incidence of cyanobacteria biofilms has increased in recent years despite no significant intensification of land use in the catchment. So I wonder whether there is a temporal dimension to eutrophication which needs investigation. Does Microcoleus need to be seeded from somewhere? How does it arrive in a freshwater ecosystem? Given its apparent reliance on changing pH and dissolved oxygen for release of trapped phosphorus to enable its proliferation – in a low P environment – it appears that measures such as river shading and occasional flushing from upstream water storage would be useful control measures.

    • Yes. Seeding is important. Our collaborator at the Cawthron Institute (Susie Wood) has worked extensively with Microcoleus and has found that under experimental growth conditions rapid growth requires seeding from small quantities of prior growth on cobbles. So if Microcoleus is a minor biofilm member on the riverbed under normal conditions (which should be its usual state), it should be well positioned to proliferate when surplus nitrogen is introduced. However, we would need historical monitoring data to establish whether Microcoleus presence in normal riverbed biofilms changed through time.

      Regarding the temporal aspect, Microcoleus proliferation events do tend to occur more frequently in summer when conditions are drier and there is ample sunlight (although too much sunlight can be damaging – overloading the photosynthetic apparatus). While rainfall is important for flushing nutrients into our waterways (which prompt cyanobacterial blooms), heavy rainfall, which is less common in summer, disrupts thick cyanobacterial mats, ending proliferation events (and our sampling work). So aside from any changes in nitrogen usage on land, season and weather patterns also matter.

      Conditions influencing the release of trapped phosphorus, such as pH and dissolved oxygen are controlled by the cyanobacteria, and are specifically internal to the mats. The cells secrete, and are embedded in, a thick and sticky gelatinous extracellular polymeric substance, which enables them to create a chemically very unique environment within biofilms (or thicker mats), even when within a river of flowing water. As they are constantly being subjected to flowing water that is already very distinct chemically and low in phosphorus, further flushing is unlikely to make a difference (although see note about regarding physical disruption by heavy rainfall). Permanent shading would likely have unintended ecological consequences. Temporary shading may be a bandaid approach worth considering, although this would be logistically challenging given the spatial extent of some proliferations, and would need to take into account other ecological effects (even if transient) and the fact that cyanobacteria do not necessarily thrive in intense sunlight (i.e. partial shading may not work).