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Questions of Quillwort biogeography

NIWA uses genetic studies to unravel what quillwort species we have in our lakes and where they are found.

Quillworts (Isoetes) are spiky-looking, submerged plants that grow as turfs in shallow, clear waters of lakes in New Zealand. These are a plant genus more closely related to ferns than to higher plants, and they number about 200 species world-wide. Unfortunately, our endemic quillworts are disappearing from some lakes due to alien weed invasions, poor water quality and resulting loss of habitat. Quillworts are now extinct in the upper half of the North Island. In the Central North Island, quillworts remain common in places such as Lake Taupo, while turfs are still abundant in many South Island lakes.

More information about lsoetes

Quillwort species prove difficult to identify due to their lack of distinguishing features! One question about quillworts is how many different species occur here in New Zealand, and where are they found? Whilst convention is that there are two species here, another expert suggests there is only one species with three varieties. More recently, polyploidy (different chromosome numbers) has been found, confirming there is previously unrecognised variation in our quillworts.

If endemic quillworts and their contribution to native biodiversity are to be preserved, it is important that we can recognise plant differences and understand their patterns of distribution. For example, how genetically distinct are the few remaining quillwort plants collected from Northland (Lake Omapere) that now exist only in NIWA’s cultures? Using genetic tools we hoped to be able to answer such quillwort questions.

Our study investigates quillwort populations collected over different geographical scales. Plants were sampled from 20 lakes across New Zealand to give a broad scale of variation. At a smaller spatial scale, quillworts were taken from six sites within four large lakes. At the smallest scale, plants were collected from different depths at each of the sites.

Two levels of genetic (DNA) analyses were used. Firstly we looked at DNA sequence data (ITS (internally transcribed spacer sequence), rbcL and trnL introns) that are expected to reveal differences at higher taxonomic levels, such as species. Secondly, we followed by using RAPDs (Random amplified polymorphic DNA), which are recognised as population-level markers.

Our results to date indicate genetic differences across quillwort biogeography with both levels of analyses. We identified a separate South Island group of quillworts, while the plants from Lake Omapere in Northland were also separated. As this plant is almost certainly extinct at Lake Omapere, preservation of these cultures is important. Additional studies are planned with different genetic markers to corroborate our findings.

Our results to date (PDF 854 KB)


Funding for this ongoing study has been provided by FRST, with funding for a pilot study provided by the Department of Conservation. We also thank Donald Britton (University of Guelph, Canada), Daniel Brunton (D Brunton Consulting Services, Canada) and Carl Taylor (Milwaukee Public Museum, USA) for sharing their findings with us.

Protecting and restoring Waikato peat lakes


The 31 peat lakes of the Waikato region are the largest group of lakes of this kind in New Zealand. Their catchments contain peat deposits and, as a result lake waters are typically brownish in colour and mildly acidic due to the presence of leached humic substances. However, the unusual characteristics of these lakes make them valuable habitats for many unique plant and animal species.

Two significant peat lake systems in the region are Lakes Rotomanuka North (12 ha) and Rotopiko (Serpentine) North (1.5 ha), located just north of Te Awamutu. Both lakes are remnants of once larger lakes (Lake Rotomanuka and Lake Rotopiko) whose water levels fell because of human activities (catchment drainage works and the construction of outflow channels). Lake Rotomanuka became two distinct water bodies (Rotomanuka North and South) and Lake Rotopiko became three (Rotopiko North, South and East).

Rotomanuka North and Rotopiko North are shallow and nutrient-rich (eutrophic), and have pastoral catchments with intensive dairy farming. However, the state of the aquatic vegetation in the two lakes is very different. Rotomanuka North is now devegetated following the catastrophic collapse of the submerged vegetation, predominantly oxygen weed (Egeria densa) beds, and a deterioration in water clarity in the period 1996–2000. In contrast, Rotopiko North is one of only a small number of lakes regionally, and nationally, to retain solely native aquatic vegetation.

Pest fish control in Rotopiko (Serpentine) North

Unfortunately, recent lake surveys have shown that the pristine condition of Rotopiko North is now threatened. The discovery of the herbivorous pest fish, rudd (Scardinius erthrophthalmus) by regional council (Environment Waikato) staff in nearby Rotomanuka North in 2001 sparked further investigations that later confirmed its presence in the adjacent Rotopiko complex.

Recent vegetation surveys provide further indications that Rotopiko North is a system under ecological stress. In summer, stratification and severe attached and planktonic algal growths result in the die-off of large areas of charophytes. So far, the vegetation has been able to recover in the winter months. However, the presence of rudd in this lake is of major concern since grazing by herbivorous fish is an additional stress factor that may ultimately contribute to the collapse of the vegetation, similar to that which has occurred in Rotomanuka North, Rotopiko South, and many other small lakes in the region.

Following the discovery of rudd, an Environment Waikato-NIWA-Department of Conservation working group promptly devised a strategy to reduce rudd abundance in the Rotopiko Complex. This strategy has involved erecting specially designed temporary weirs to prevent fish passage in drains between the waterbodies and an extensive netting programme to capture and remove rudd from the lakes. Netting operations have so far been undertaken in September 2001 and March 2002, with another planned for September 2002. So far, a total of 1140 rudd have been removed and, encouragingly, the catch was more than halved (823 to 317) and large fish were absent in the second operation.

In conjunction with the eradication strategy NIWA staff are conducting seasonal vegetation surveys of the Rotopiko waterbodies to assess whether rudd removal is proving effective in enhancing the condition of the aquatic plant communities, and to establish how long the degraded “summer” condition persists. Vegetation surveys have so far been carried out in February and June 2002 and two more are planned for August and November 2002. Although seasonal variation in lake condition has so far made data interpretation difficult, results are encouraging. In Lake Rotopiko North, large areas of seedlings and small charophyte (Nitella cristata) plants below 3 m depth in June 2002 suggests an improvement in lake condition relative to a previous survey in July 2001. However, confirmation of these trends is needed from subsequent surveys planned for later this year.

Revegetating Rotomanuka North

Environment Waikato and Department of Conservation are also working on the restoration of Rotomanuka North. Re-establishment of aquatic vegetation in the lake is considered highly desirable because of the ecosystem and water quality benefits that would result. At present the degraded water clarity of the lake may prevent plant recovery but initiatives in the catchment or lake (e.g. reducing sediment and nutrient inputs, removal of pest fish) might improve this in the future.

On behalf of Environment Waikato, NIWA recently undertook a study to assess the state of the sediment seed bank in this lake in order to determine whether natural regeneration of submerged aquatic plants might be possible under suitable conditions. Specifically, the aim of the research was to evaluate a number of attributes of the lake sediment seed bank including seed density and distribution, seed species composition and seed responsiveness under conditions suitable for germination.

A large number of sediment cores (120) were collected from depths of 1.5 to 4 m at six sites around the lake in November 2001. At NIWA, cores were placed outdoors, in a suitable depth of water (0.8 m) and under suitable light conditions for germination (~8% natural light). After 3 and 6 months, the cores were examined for any germinating seedlings. At the end of the 6-month period seeds were extracted from core subsamples to determine viable seed density and distribution and identify the contributing plant species.

The submerged plant species represented in the sediment seed bank were predominantly charophytes. Most of the viable seed (89%) was derived from one species, Nitella pseudoflabellata. Other charophytes represented were Chara corallina, C. globularis, N. leptostachys and N. hyalina. A very small proportion of the seed (<1%) was from the Pondweed species, Potamogeton cheesemanii. The three most abundant plant species, N. pseudoflabellata, C. corallina and N. leptostachys were widespread across the sampled sites but the other species were not.

Despite the presence of viable seeds, no seedlings germinated from cores in the six-month period. This demonstrates that the potential for natural regeneration of submerged plants from the sediment seed bank in Lake Rotomanuka North is low. The most likely reason for this is considered to be the very low density of viable seeds in the sediment. The median viable seed density was 1500 seeds per square metre, which is only 2% of that found beneath native vegetation in lakes. However, the value is similar to that found for other lakes that have undergone a submerged plant decline or lakes dominated by introduced oxygen weed (Hydrocharitacean) vegetation (which reproduces vegetatively and can exclude other seed-producing plants). Other possible reasons for the lack of seed germination were identified and include seeds being too old or in poor condition, seeds being buried too deep, or the large amounts of litter from emergent rush plants (Typha orientalis and Eleocharis sphacelata) inhibiting germination.

Future directions

The above studies on Lakes Rotomanuka North and Rotopiko North serve to highlight the notion that ecosystem protection is easier than ecosystem restoration. Once devegetated, shallow lakes are inherently hard to revegetate. This is because the collapse of submerged vegetation invariably results in a lake entering an ‘alternative stable state’ of low water clarity, dominated by algae or containing high levels of suspended sediment, that then inhibits any recovery of submerged plants. In the case of Rotomanuka North, the lack of a viable seed bank means that, even if water clarity could be improved, natural regeneration of aquatic vegetation is not an option for this lake. The next task is to determine whether suitable transplant species and techniques can be identified for this lake. For Rotopiko North the short term acute risk of rudd damage to the vegetation is under control provided fish removal is continued or an eradication attempt is made. However, the stability of the vegetation through summer conditions is still an issue that needs attention.

Tony Dugdale, Mary de Winton and Fleur Matheson

Further reading:
Barnes, G.E. (2001). Aquatic and marginal vegetation of Lake Serpentine North. Environment Waikato Technical Report No. 2001/03.
Barnes, G.E. (2002). Water quality trends in Lake Rotomanuka North. Implications for restoration and management. Environment Waikato Technical Report No. 2002/03.
Speirs, D., Barnes, G. (2002). Fish populations of Lake Rotomanuka 2000 and 2001. Environment Waikato Technical Report 2001/07.

Charophytes and clear water: cause or consequence?

As part of our Visiting Scientist programme, NIWA hosted Dr Michelle Casanova from Australia, an expert on the ecology of charophytes (macro-algae). Michelle investigated a known phenomenon that the clearing of turbid lakes is often linked to a sudden appearance by charophytes. The question was: do these small plants in fact aid in clarifying turbid waters, or did they simply establish only when water clarity increases? The relationship between turbidity and charophyte germination and subsequent growth was tested.

Charophytes were found to be more effective at reducing turbidity (per unit surface area) than the control (plastic plants) or hornwort. Charophyte ‘seeds’ (oospores) also germinated equally well in highly turbid water as in clear water, despite an estimated three-fold difference in the level of light for germination.

These results are of particular relevance in directing focus towards manageable barriers that may interfere with vegetation restoration objectives. Experimental demonstration of the effectiveness of high charophyte plant cover at clearing turbid waters has significance in ensuring management strategies recognise the important role played by this group of plants.

For more information see de Winton, M (1999). Restoring water plants. Water & Atmosphere 7(4): 9–11.

Bryophytes add biodiversity to lakes

A recent review of information on bryophytes (mosses and liverworts) confirms that they are the deepest growing macrophytes in New Zealand lakes. While these ‘deep-water’ bryophytes are known from a few lakes elsewhere in the world, NZ has some of the deepest records ever – probably due to the pristine nature of some of our clear-water lakes.

NIWA’s Dr John Clayton was amongst the first to confirm the presence of deep-water bryophytes in NZ while scuba diving in Lake Wakatipu off Sunshine Bay in 1979. For the first time bryophytes were found growing as a distinct community extending into deeper water beyond the well known charophyte meadows that are so common in many clear-water lakes. This important discovery led to a deep-diving exploration to determine whether other deep clear-water lakes also had bryophytes.

One of the most fascinating discoveries was in Lake Coleridge in 1980. Dr Clayton had previously carried out an underwater scuba survey in 1978, but only charophytes were ever found growing down to a maximum depth of 35 m. The question being pondered was whether previously he had never dived deep enough! This time he dived beyond the 35-m deepest boundary only to see bare mud. But as he dived even deeper into the twilight zone he saw what he was looking for – the first signs of bryophytes just beginning at 40 m. As he descended even further this then became a complete carpet of mosses and liverworts, which extended to an astounding 70-m depth! These early observations were met with some scepticism by some plant researchers, who suggested the records stemmed from debris washed into lakes from streams.

Over 25 years, NIWA scientists gathered a wealth of records for these tiny plants and some extensive collections. These formed the basis of a collaborative study with one of New Zealand’s foremost authorities on mosses, Dr Jessica Beever (see Landcare Moss Flora, and also involved other bryophyte experts.

The results were exciting. Altogether 16 NZ lakes had bryophytes growing at 10-m depth or more (see Table). These lakes had very clear water and the depth that bryophytes grew to closely reflected how much light penetrated through the water.

Table of lakes and maximum depth records for deep-water bryophytes.

Lake Bryophyte
depth (m)
Lake Bryophyte
depth (m)
Alta 12 Tennyson 30
Manapouri 14 Sumner 32
Te Anau 17 Hawea 35
Hauroko 19 Wanaka 50
Monowai 22 Waikareiti 50
Ohau 22 Lochnager 57
Rotoiti 22 Wakatipu 60
Rotoroa 22 Coleridge 70

Some 34–42 mosses and liverworts were found at 10-m depth or more. Some of these could not be identified because of their odd development in these environments. For example, several resembled green string!

The deep-water bryophytes were never fruiting and apparently relied on vegetative growth. Their initial source would have been the bryophyte communities found in the forests, tussocklands and streams of the lake catchments.

The study concluded that bryophytes could grow at the bottom of lakes because they are so successful at tolerating stress, in this case the extremely low light levels. They are not so good at competing with bigger, more robust plants, so bryophytes only dominated at deep depths where the larger plants could not survive. Neither are bryophytes tolerant of disturbance, and so did not occur in North Island lakes where foraging crayfish (koura) were numerous.

Bryophytes greatly extend the zone of vegetation in some clear-water lakes; they contribute additional biodiversity, and enhance habitat complexity in our lakes. Unfortunately, these unusual plant communities will be the first to disappear should the clear-water lakes become turbid from nutrient enrichment. Their survival depends on how well NZ’s pristine lakes are protected for the future.

Further reading

de Winton, M.D.; Beever, J.E. (in press). Deep-water bryophyte records from New Zealand lakes. New Zealand Journal of Marine and Freshwater Research 38(2).

Special thanks go to Jessica Beever for extensive identifications of specimens and collaboration on the publication; Allan Fife (Landcare Research), the late Dame Ella Campbell (Massey University), John Braggins (Auckland Museum), Elizabeth Brown (Royal Botanical Gardens and Domain Trust, Sydney) and Bryony Macmillan (CHR) for additional identifications.
Work was funded by the New Zealand Foundation for Research, Science and Technology (C01X0221). Lake surveys were co-funded by the Department of Conservation, Meridian Energy and TrustPower Ltd. Numerous NIWA divers braved cold, dark waters to collect bryophyte data and specimens over the years.

Charophyte diversity – species clarification and new records in NZ

Charophytes (Order Charales) are a group of submerged plants found in aquatic habitats all over the world. Although they are macro-algae, charophytes resemble higher plants in their appearance (Image 1) and indeed genetic studies reveal them to be the closest living relatives of land plants (Karol et al. 2001).

More information on Charophytes

In New Zealand, charophytes are the most ubiquitous of native freshwater plants and they receive special recognition as a beneficial component of lake ecosystems. Nevertheless, they are often difficult to identify to species level and some confusion exists as to which species are present in this country. This problem is being addressed within the biodiversity component of NIWA’s Aquatic Plant Management Programme.

Identity parade

One aspect of our research is to find consistent species characteristics that can be used to separate and identify the array of 16 known species in NZ. We have found combinations of plant architecture, branchlet cell stucture and other features that provide the best clues to charophyte identity and these are illustrated in easy-to-use guides (Image 2) that have been used at workshops for aquatic plant identification. Other aids to identifying charophytes are the size, shape and ornamentation of their oospores (sexual propagule) and we have developed a key to NZ species for future publication (Image 3).

Biodiversity roll call – what is here

One species of charophyte, Nitella hookeri, was chosen for a focused study. N. hookeri is common in NZ but rare overseas and so it provides a unique flavour to our largely Australian charophyte assemblage. This species displays a wide variation in morphology and some specimens are easily confused with the similar species N. cristata. Was there more than one distinct entity included in this complex species? A contributing factor to uncertainty surrounding N. hookeri was the misplacement of the original type specimen (dried herbarium plant) from Kerguelen Island, Indian Ocean, upon which the description of the species was based (Wood & Mason 1977).

More information about Nitella hookeri

We approached the problem from four angles.

  • Widely differing examples of N. hookeri were collected from all over the country and then cultured under identical conditions to see if morphological differences were environmental or genetic.
  • Dr Michelle Casanova, a charophyte expert from the University of New England, Australia, examined dried specimens of these plants and compared them to Australian and NZ specimens borrowed from national and overseas herbaria. During this latter work the missing type specimen was found! Up to seventy plant characteristics were measured and multivariate analyses used to separate out plant types.
  • We also undertook chromosome counts to see if these distinguished different entities (Image 4).
  • The final component of the study was genetic analyses in collaboration with Dr Ken Karol, University of Maryland. Dr Karol analysed DNA sequence data from the rbcL (plastid) genome to show how different or similar this genetic character was amongst the group.


When we pulled all the strands of evidence together, it was apparent that there are two distinct plants that have been lumped together as Nitella hookeri. Dr Casanova concludes that an earlier name should be re-instated for one of these plants – Nitella tricellullaris, creating an endemic charophyte record for NZ. Moreover, the inclusion of the similar species Nitella cristata in the analyses has shown it differs from the classic examples of that species and that the identity of this plant in NZ and Southern Australia needs to be investigated further.

Making records

One spin-off from our study was the discovery of another charophyte species in NZ! During N. hookeri collections, an unusual looking charophyte was retrieved from an isolated South Island lake. Out of interest, it was included in a shipment of material for genetic analysis and Ken Karol was able to confirm that the plant was genetically identical to a species Nitella subtilissima in Australia. Subsequently, culture and new collections showed the plant to have characteristics in keeping with this species ID and we are now keeping an eye out for new sites and ecological information.

Further reading

Karol, K.G.; McCourt, R.M.; Climino, M.T., Delwiche, C.F. (2001): The closest living relatives of land plants. Science 294: 2351–2353.
Casanova, M.T. (2002). The taxonomic status of Nitella hookeri A. Braun and N. cristata in New Zealand and Australia. Report to NIWA, 25 p.
Wood, R.D.; Mason, R. (1977). Characeae of New Zealand. New Zealand Journal of Botany 15: 87–180.
Champion, P.D.; de Winton, M.D. (2002). New Zealand charophytes. In: Aquatic macrophytes in rivers. Manual for the Biodiversity Identification Workshop series, pp. 18–23, 38–40.

Impact of fish on plant survival

Rudd are freshwater fish similar in appearance to large goldfish, except they have red fins. They were illegally imported to New Zealand in the 1960s and are now well established as large populations in many waterbodies from the Waikato north.

Rudd eat aquatic plants and when in high numbers, in relation to the quantity of aquatic vegetation, may have significant unwanted impacts on the aquatic environment. They are now being implicated with degrading stressed freshwater ecosystems with a 'top down' effect impacting on most aquatic biota.

In the Waikato, most large water bodies have been degraded by a loss of plant species diversity over the last two decades. Many, such as the hydro-electric lakes, have become dominated by the aquatic plant hornwort (Ceratophyllum demersum) while others have lost all their submerged vegetation.

While excessive plant growth can be a nuisance by interfering with recreational activities, accumulating on lake shores, blocking water intakes, or causing overnight oxygen depletion, a 'weed' growth is usually preferred to an algal nuisance. The switch from a plant-dominated waterbody has consequences for many other species. Invertebrates associated with aquatic plants disappear or are markedly reduced in number and this can affect some fish species. Waterfowl (especially the herbivorous black swan) have also been affected, resulting in a large reduction in numbers.

Agencies such as the Department of Conservation and Fish & Game are now actively seeking to restore aquatic habitats where possible. A joint NIWA/Waikato University/Fish & Game New Zealand program has been looking at the feeding rates and preferences of rudd.

Feeding experiments of seven aquatic plant species in outdoor tanks showed rudd had marked likes and dislikes. Rudd consume large amounts of species such as nitella and pondweed (Potamogeton) which are soft relative to the coarse tough foliage of hornwort. Potential impacts of rudd in water bodies may therefore be far greater for the species much preferred by rudd. To test this a range of aquatic plants was put out overnight on mid-water booms in Lake Karapiro near a dense bed of hornwort. As would be predicted from the outdoor selectivity experiments, the nitella disappeared and most of the pondweed and elodea (Elodea canadensis) was grazed, whereas egeria (Egeria densa) showed little grazing and hornwort was not touched. These experiments were repeated on different occasions and an underwater video camera was also set up to monitor any feeding and disturbance activity. The results obtained indicate that grazing pressure is assisting hornwort to remain the dominant submerged plant.

Deborah Hofstra and Rohan Wells

Adapted from: Wells, R.D.S. (1999). Lake vegetation restoration – are Rudd an ecological threat? Water & Atmosphere 7(4): 11-13.


Endemic quillworts have spiky appearance, grow to 0.3 m tall, and reproduce by spores in the leaf base (Photo: Rohan Wells)
Endemic quillworts have spiky appearance, grow to 0.3 m tall, and reproduce by spores (see arrow) in the leaf base (Photos: Rohan Wells; Trevor James, AgResearch)
Quillworts collected from across a depth range at a site give fine scale information on genetic variation within lake populations (Photo: John Clayton)
In RAPDs the DNA components are separated within a gel and patterns in band presence (see arrow) indicate genetic relatedness (Photo: Deborah Hofstra)
Quillworts from lakes of different regions show geographic patterns of relatedness based on the RAPDs method of genetic analyses. More genetically similar populations occur on shorter 'branches'.
Lake Rotomanuka North. [P. de lange]
Lake Rotopiko (Serpentine) North. [P. de Lange]
Charophyte oospores (‘seed’). (Photo: M. De Winton)
John Clayton samples a luxuriant carpet of bryophytes at 20-m depth in Lake Rotoroa, Nelson. (Photo: R. Wells)
Bryophyte community at 20-m depth in Lake Rotoroa - a closer view of this diverse community. (Photo: R. Wells)
Mary de Winton retrieves a sample of bryophytes from 40-m depth in Lake Wakatipu. (Photo: R. Wells)
Close-up photos of some moss species found deep within lakes, including one with minute, scale-like leaves. (Photos: M. de Winton)
Streams draining to Lake Wakatipu had rich communities of bryophytes – one likely source of the deep-water assemblage. (Photo: J. Clayton)
Image 1 - Charophytes have upright stems and regular whorls of branches that give the appearance of a higher plant, but they are actually macro-algae. (Photo R. Wells)
Image 2 - Extract from a guide for identifying charophytes in NZ waters. (Champion & de Winton 2002)
Image 3 - Scanning electron images showing variation in oospore size, shape and ornamentation between six Nitella species. (A-F)
Image 4 - A preparation of stained chromosomes from a charophyte cell (male fruiting body) viewed at 1000 x magnification.
Rudd (Scardinius erythrophthalmus). (photo by D. Rowe)