Biofilms in groundwater systems


Biofilms – communities of microorganisms growing together – are common in groundwater systems, but we don't know much about them. Our scientists devised a series of studies to start to understand what environmental changes they can cope with and still play their role in a healthy groundwater ecosystem. 

The issue

Microorganisms growing in communities which are attached to surfaces are called biofilms (Figure 1).

The individual organisms which make up the biofilm are embedded in a mesh of polymers which makes the biofilm community very resilient to their environment. Biofilm communities use nutrients from the surrounding environment to grow larger (make more cells) and to generate energy for carrying out their metabolic functions

Biofilms are found throughout the natural world - they are present in soils, sediments, rivers and lakes. Recent studies have also shown that biofilms can be found in groundwater systems; however, the inaccessibility of groundwater ecosystems makes them difficult to study and available data on the biology and ecological function of the biofilms are scarce.

The primary producers in groundwater ecosystems are heterotrophic – they can't make their own food/energy, unlike plants and algae – and are dominated by bacteria and Archaea. The reliance of groundwater biofilms on these microbes is one of the major differences between groundwater systems and surface water ecosystems, where the primary producers are dominated by autotrophic organisms (plant and algae), which use sunlight as their energy source.

Lack of knowledge about groundwater biofilm communities

The National Objectives Framework, which the Government is developing as part of its reform of freshwater management, aims to set limits for different freshwater systems within New Zealand in order to ensure the protection of their 'life-supporting capacity'. Groundwater ecosystems, which include biofilm, protozoan and macro-invertebrate communities, are part of the 'life-supporting capacity' of New Zealand's aquifers. However, there is not, at present, sufficient information available for these groundwater ecosystems to develop such limits. This research project on biofilms in groundwater systems will assist in provision of this information.

Groundwater biofilms are thought to play a role in nutrient processing, and there is likely to be a complex interaction between biofilm growth and grazing by higher organisms such as protozoa and invertebrates. However, little information is available on these interactions, and the ecosystem roles and functions are speculative rather than substantiated by experimental studies.

There is also concern about how changing environmental conditions, such as fluctuations in groundwater levels, might affect groundwater ecosystems. To date, though, no substantiated information is available.

The solution

We have been carrying out some investigative work on groundwater biofilm communities.

The first requirement was to develop techniques for sampling groundwater biofilms, and sensitive methods for analysing biomass and activity of the bacterial cells in the biofilm.

Natural gravel was used as the attachment medium to mimic the groundwater environment (Figure 2). It was put into nylon bags and placed in wells to allow colonisation by microbes - the biofilm communities generally took 3-5 months to develop.

The biofilms were then analysed for biomass and activity using a range of different tests – you can find out more about them in Williamson et al. (2012). Biofilm growth chambers in the laboratory were developed so that biofilm communities could be grown under controlled conditions that would be the same as the groundwater environment (no light, a constant temperature in range of 12 – 16 oC, similar flow velocities and levels of nutrients in the water).

The results

Study one – the effects of nutrients on biofilm biomass and activity

Our first study aimed to collect basic information (previously not available) on how fast the biofilms grew and how they responded to different concentrations of the major nutrients – nitrate, dissolved reactive phosphorous (DRP) and dissolved organic carbon (DOC).

We put gravel into four wells in the Selwyn catchment along a nutrient gradient - nitrate concentrations increased down the gradient, but DRP and DOC decreased.
We found that biofilm biomass and activity decreased along the gradient, correlating with the DRP and DOC levels, which were determined to be the limiting nutrients in this environment.

Study two – the effects of drying out (desiccation)

The second study was designed to look at the effects of a dry period on biofilm biomass and activity, to mimic the effects of fluctuating groundwater levels. Groundwater levels fluctuate naturally due to the seasonal variation of recharge (which occurs mostly during winter), but the range of fluctuations is likely to increase with the increasing development of irrigation from groundwater sources.

Gravel samples were again placed in wells near Leeston, Central Canterbury, and in laboratory biofilm growth chambers and left to allow biofilms to establish. Some of the samples were then lifted and suspended above the water table (in the field) or the growth chambers were drained (in the laboratory).

The dry period chosen was 4 months; at the end of this period the samples were rehydrated.

Samples were analysed before desiccation, after 4 months' desiccation, 1 month following rehydration, and 3 months following rehydration. Analysis of the biomass and activity data indicates that the biofilm communities are fairly resilient to periods of 4 months' desiccation. Some of this resilience would be due to the relatively high humidity just above the groundwater table, which is in marked contrast to the low humidity, high sunlight environment that often characterises a dry period for a surface water environment.

Study three – nutrient processing and grazing

The third study, currently under way, is designed to look at the role of biofilms in processing nutrients. It is also investigating the role of protozoa and macro-invertebrates in grazing the biofilm communities, in order to maintain the groundwater system's porosity (a measure of how much water can be stored) and ability to transmit water.

Biofilms will be grown in laboratory growth chambers under high nutrient conditions which will stimulate biofilm growth and cause clogging of the groundwater system. The study will include the addition of protozoa and macro-invertebrates, in order to assess the impacts of grazing on the biofilm communities on the hydraulic conductivity (as a measure of porosity and water transport ability) of the system.

You can see an example of biofilm grown on gravel under high nutrient conditions in Figure 3.


Williamson, W. M., Close, M. E., Leonard, M. M., Webber, J. B. and Lin, S. (2012), Groundwater Biofilm Dynamics Grown In Situ Along a Nutrient Gradient. Ground Water, 50: 690–703. DOI:  10.1111/j.1745-6584.2011.00904.x

NIWA Contacts

Principal Scientist - River and Coastal Geomorphology
External people involved: 
Murray Close, ESR
Louise Weaver, ESR
Aynsley Hickson, Scion
Judith Webber, ESR
Wendy M. Williamson, ESR
Page last updated: 
4 October 2016
Figure 1. Biofilm composition. Individual cells, which may be of the same species (plain cells) or different species (coloured cells). The microbial community is surrounded by a mesh of polymers (pale green) that is secreted by microbes upon attachment to a surface or each other.
Figure 2. Washed, fine (2.8 mm diameter) gravel used as the attachment medium for growing biofilms. Scale is a 1 ml orifice pipette tip, which is 70 mm long. [NIWA]
Figure 3. Biofilm communities on gravel after clogging experiments (Study three) in the biofilm growth chamber. [NIWA]