The role of experimental microcosms in ecological research

A number of recent and important developments in community ecology have been derived from experiments conducted in microcosms. Studies with microcosms have addressed a broad range of phenomena, including climate change, biodiversity, assembly rules, habitat restoration, trophic dynamics and mycorrhizal associations. The common factor linking these studies is that they manipulate an individual environmental axis and explore the role that axis plays in structuring communities. We discuss six recent studies to illustrate the use and design of microcosms for community ecology research.     

Bryophyte flora and vegetation of serpentine sites in the French Massif Central

Eight major serpentine sites in the French Massif Central have been bryofloristically surveyed and their specific assemblages studied by performing systematic relevés. Seventy bryophyte taxa are reported from these serpentine areas. Archidium alternifolium, Bryum gemmilucens, Cephaloziella stellulifera, Grimmia dissimulata, Racomitrium fasciculare, R. lanuginosum and Riccia subbifurca are dominant and characteristic species. Soil and rock communities harbour typical combinations of specialized and ubiquitous taxa. The occurrence of saxicolous species (Grimmia) on the ground may be a typical feature of serpentine communities. The scarcity of liverworts is underlined, as is the complexity of the controlling factors. Lack of competition and periodic submergence are probably ecological factors of prime importance. Successional pathways are certainly insufficiently known, especially as far as bryophytes are concerned. The causes of negligible succession on skeletal soils would benefit from renewed studies. Grazing of serpentine grasslands, generally considered the most relevant management tool, should be evaluated further.     

Water stress,leaf nutrients and defoliation: a model of dieback of rural eucalypts

Water stress, concentrations of foliar nutrients and damage of foliage by insects were studied over an eleven month period, for eight dieback eucalypts and eight closely matched healthy trees growing in close association on two grazing properties near Brisbane. Four healthy eucalypts in a neighbouring State Forest were also studied. The study region had suffered severe climatic stress between 1972 and 1976 when dieback was first observed by residents and when high populations of defoliating insects were observed. Dieback trees had a higher proportion of foliage damaged by insects and higher concentrations of foliar nutrients than did matched healthy trees. The study period was one of low climatic stress during which dieback and healthy trees followed similar seasonal patterns of predawn xylem pressure potential. Dieback trees developed lower daytime minimum xylem pressure potentials than did matched healthy trees, and differed in their stomatal responses. A model of initiation and development of rural eucalypt dieback is proposed. This may have general application to many non-specific rural diebacks in which heavy insect damage is implicated. The balance between rural eucalypts and their insect herbivores is precarious. Any factor capable of causing extensive defoliation, or an increase in foliar nitrogen, or an increase in populations of insect herbivores may upset this balance. A positive feedback loop may be activated, whereby the production of nitrogen rich epicormic foliage enhances a build up of insect populations. Repeated insect defoliation leads to tree dieback. Evidence in the literature supporting the model is reviewed and aspects requiring further research are outlined.     

Linking above-ground and below-ground effects in autotrophic microcosms: effects of shading and defoliation on plant and soil properties

Although factors affecting plant growth and plant carbon/nutrient balance – e.g., light availability and defoliation by herbivores – may also propagate changes in below‐ground food webs, few studies have aimed at linking the above‐ground and below‐ground effects. We established a 29‐week laboratory experiment (～one growing season) using autotrophic microcosms to study the effects of light and defoliation on plant growth, plant carbon/nutrient balance, soil inorganic N content, and microbial activity and biomass in soil. Each microcosm contained three substrate layers – mineral soil, humus and plant litter – and one Nothofagus solandri var. cliffortioides seedling. The experiment constituted of the presence or absence of two treatments in a full factorial design: shading (50% decrease in light) and artificial defoliation (approximately 50% decrease in leaf area in the beginning of the growing season). At the end of the experiment a range of above‐ground and below‐ground properties were measured. The shading treatment reduced root and shoot mass, root/shoot ratio and leaf production of the seedlings, while the defoliation treatment significantly decreased leaf mass only. Leaf C and N content were not affected by either treatment. Shading increased NO ₃–N concentration and decreased microbial biomass in humus, while defoliation did not significantly affect inorganic N or microbes in humus. The results show that plant responses to above‐ground treatments have effects which propagate below ground, and that rather straightforward mechanisms may link above‐ground and below‐ground effects. The shading treatment, which reduced overall seedling growth and thus below‐ground N use and C allocation, also led to changes in humus N content and microbial biomass, whereas defoliation, which did not affect overall growth, did not influence these below‐ground properties. The study also shows the carbon/nutrient balance of N. solandri var. cliffortioides seedlings to be highly invariant to both shading and defoliation.     

Bryophyte vegetation in a wooded meadow: relationships with phanerogam diversity and responses to fertilisation

In the Laelatu wooded meadow in Estonia, famous for its phanerogam diversity, the bryophyte community has been investigated in order to compare its flora and diversity relationships with those of the vascular plant community. Ninety-six bryophyte species were found, 13 of them are hepatics; the majority of the bryophytes are epigeic species common to meadows and forests, including many calciphilous species. Vascular plants and bryophytes display opposite responses to fertilisation. For vascular plants, fertilisation increases the coverage and diminishes the number of species, while for bryophytes it diminishes coverage and increases the number of species. The relationship between the number of species in small plots and the total number of species in the area is similar for vascular plants and bryophytes. No significant changes in the bryophyte community in Laelatu wooded meadow has been detected during the last 30 years.     

Interactions between algae and the microbial loop in experimental microcosms

We conducted a short-term microcosm experiment to study the direct and indirect effects of a bacterivore on bacteria and the dynamics of two species of green algae. We introduced Scenedesmus , Chlorella and Colpidium , a bacterivorous ciliate, successively in a carbon-rich medium. Bacteria were introduced with Scenedesmus , Chlorella and Colpidium . The experiment lasted 40 days, preventing us from detecting whether the populations had reached equilibrium. The bacterivore had a positive effect on both species of algae by limiting the abundance of bacteria. In absence of the bacterivore, bacteria did not exclude the two algal species, despite the high carbon:nutrient ratio of the medium. Unexpectedly, by the end of the experiment the bacterivore declined in all microcosms. Also, Chlorella growth was impeded by the presence of Scenedesmus . These two observations might be explained by allelopathic interactions. Our experiment suggests that the functioning of such a simple community is far more complex than assumed in previous theoretical and experimental models. Studying the dynamics of the system, however, allowed us to disentangle species interactions.     

Effects of floating vegetation on denitrification,nitrogen retention,and greenhouse gas production in wetland microcosms

Wetlands are biogeochemical hotspots that have been identified as important sites for both nitrogen (N) removal from surface waters and greenhouse gas (GHG) production. Floating vegetation (FV) commonly occurs in natural and constructed wetlands, but the effects of such vegetation on denitrification, N retention, and GHG production are unknown. To address this knowledge gap, we used microcosm experiments to examine how FV affects N and GHG dynamics. Denitrification and N retention rates were significantly higher in microcosms with FV (302 μmol N m^?2 h^?1 and 203 μmol N m^?2 h^?1, respectively) than in those without (63 μmol N m^?2 h^?1 and 170 μmol N m^?2 h^?1, respectively). GHG production rates were not significantly different between the two treatments. Denitrification rates were likely elevated due to decreased dissolved oxygen (DO) in microcosms with FV. The balance of photosynthesis and respiration was more important in affecting DO concentrations than decreased surface gas exchange. The denitrification fraction (N₂-N production: N retention) was higher in microcosms with FV (100 %) than those without (33 %) under increased (tripled) N loading. A 5 °C temperature increase resulted in significantly lower denitrification rates in the absence of FV and significantly lowered N₂O production with FV, but did not significantly change CH₄ production or N retention in either treatment. These results suggest that intentional introduction of FV in constructed wetlands could enhance N removal while leaving GHG production unchanged, an insight that should be further tested via in situ experiments.     

Bryophyte and vascular plant species richness in boreo-nemoral moist forests and mires

We compare species richness of bryophytes and vascular plants in Estonian moist forests and mires. The material was collected from two wetland nature reserves. Bryophyte and vascular plant species were recorded in 338 homogeneous stands of approximately 1 ha in nine forest and two mire types. Regional species pools for bryophytes and vascular plants were significantly correlated. The correlations between the species richnesses of bryophytes and vascular plants per stand were positive in all community types. The relative richnesses (local richness divided by the regional species pool size) were similar for bryophyte species and for vascular plant species. This shows that on larger scales, conservation of the communities rich in species of one taxonomic plant group, maintains also the species richness of the other. The minimum number of stands needed for the maintenance of the regional species pool of typical species for the every community type was calculated using the species richness accumulation curves. Less stands are needed to maintain the bryophyte species pools (300–5300 for bryophytes and 400–35 000 for vascular plants).     

Evaluation of the effect of temperature and nutrients on the survival of Campylobacter spp. in water microcosms

Batch microcosms containing various water types (de-ionized and river water with or without sediment), incubated at a range of temperatures (5-37 degrees C), were used to facilitate a comparative evaluation of the significance of such variables and their interactions upon the collective and individual survival of four species of thermophilic Campylobacter. All variables significantly influenced (P < = 0.031) population decay rates. Minimal decay for the group was identified at low temperatures (5 degrees C) in river water, i.e. nutrient-containing microcosms. Collective decay rates within river water microcosms were significantly decreased (P = 0.03) from those observed in de-ionized water, particularly at environmental temperatures (5 and 15 degrees C). However, the increased nutrient levels observed in sediment-containing microcosms did not significantly (P = 0.41) reduce population decay rates. Overall, Camp. jejuni populations demonstrated the most resilience to the environmental stressors evaluated, with the exception of 15 degrees C where Camp. lari was the most persistent. Campylobacter coli and Camp. upsaliensis demonstrated comparable survival characteristics but were less resilient than Camp. jejuni and Camp. lari. These observations identify the suitability of water systems as a reservoir and medium for Campylobacter infection, and potentially identifies Camp. jejuni and Camp. lari as the main protagonists of water-mediated campylobacteriosis.     

Flocculation onset in Saccharomyces cerevisiae: the role of nutrients

AIMS: To examine the role of the nutrients on the onset of flocculation in an ale-brewing strain, Saccharomyces cerevisiae NCYC 1195. METHODS AND RESULTS: Flocculation was evaluated using the method of Soares, E.V. and Vroman, A. [Journal of Applied Microbiology (2003) 95, 325]. For cells grown in chemically defined medium (yeast nitrogen base with glucose) or in rich medium (containing yeast extract, peptone and fermentable sugars: fructose or maltose), the onset of flocculation occurred after the end of exponential respiro-fermentative phase of growth being coincident with the attainment of the lower level of carbon source in the culture medium. Cells, in exponential respiro-fermentative phase of growth, transferred to a glucose-containing medium without nitrogen source, developed a flocculent phenotype, while these carbon source starved cells, in the presence of all other nutrients that support growth, did not flocculate. In addition, cells in exponential phase of growth, under catabolite repression, when transferred to a medium containing 0.2% (w/v) of fermentable sugar (fructose or maltose) or 2% (v/v) ethanol, showed a rapid triggering of flocculation, while when incubated in 2% (v/v) glycerol did not develop a flocculent phenotype. CONCLUSIONS: The onset of flocculation occurs when a low sugar and/or nitrogen concentration is reached in culture media. The triggering of flocculation is an energetic dependent process influenced by the carbon source metabolism. The presence of external nitrogen source is not necessary for developing a flocculent phenotype. SIGNIFICANCE AND IMPACT OF THE STUDY: This work contributes to the elucidation of the role of nutrients on the onset of flocculation in NewFlo phenotype yeast strains. This information might be useful to the brewing industry, in the control of yeast flocculation, as the time when the onset of flocculation occurs can determine the fermentation performance and the beer quality.     

Long-term ozone effects on vegetation, microbial community and methane dynamics of boreal peatland microcosms in open-field conditions

To study the effects of elevated ozone concentration on methane dynamics and a sedge species, Eriophorum vaginatum, we exposed peatland microcosms, isolated by coring from an oligotrophic pine fen, to double ambient ozone concentration in an open‐air ozone exposure field for four growing seasons. The field consists of eight circular plots of which four were fumigated with elevated ozone concentration and four were ambient controls. At the latter part of the first growing season (week 33, 2003), the methane emission was 159±14 mg CH₄ m^?2 day^?1 (mean±SE) in the ozone treatment and 214±8 mg CH₄ m^?2 day^?1 under the ambient control. However, towards the end of the experiment the ozone treatment slightly, but consistently, enhanced the methane emission. At the end of the third growing season (2005), microbial biomass (estimated by phospholipid fatty acid biomarkers) was higher in peat exposed to ozone (1975±108 nmol g^?1 dw) than in peat of the control microcosms (1589±115 nmol g^?1 dw). The concentrations of organic acids in peat pore water showed a similar trend. Elevated ozone did not affect the shoot length or the structure of the sedge E. vaginatum leaves but it slightly increased the total number of sedge leaves towards the end of the experiment. Our results indicate that elevated ozone concentration enhances the general growth conditions of microbes in peat by increasing their substrate availability. However, the methane production did not reflect the increase in the concentration of organic acids, probably because hydrogenotrophic methane production dominated in the peat studied. Although, we used isolated peatland microcosms with limited size as study material, we did not find experimental factors that could have hampered the basic conclusions on the effects of ozone.     

子午岭典型植被凋落叶-土壤养分与酶活性特征

对黄土高原子午岭任家台林区内刺槐、油松、侧柏等3种人工林以及桦树、辽东栎等两种天然次生林的凋落叶C、N、P含量、林下土壤基本理化性质和碱性磷酸酶、脲酶、蔗糖酶3种酶的活性进行分析,并研究凋落叶C、N、P含量与土壤C、N、P含量之间的相关关系,以及土壤基本理化性质与酶活性之间的相关关系,为该区植被恢复效果评价提供科学依据与参考。结果发现:刺槐、辽东栎凋落叶碳氮比值显著低于其他植被,凋落叶分解速率相对较快;辽东栎土壤有机碳、全氮含量最高,分别为19.18、1.60g/kg,刺槐土壤全磷含量最高(0.61g/kg);土壤酶活性主要受土壤有机碳、全氮、容重及p H影响,与土壤全磷相关性不显著;人工林中,侧柏土壤中3种酶活性均高于其他植被,且侧柏凋落叶碳氮比值相对较低,分解速率较快,相比于刺槐作为造林树种更占优势。     

Small-scale distribution of interstitial nitrite in freshwater sediment microcosms: the role of nitrate and oxygen availability,and sediment permeability

The spatial distribution of interstitial NO2(-) concentrations was studied in NO3(-)-exposed freshwater sediment microcosms, using pore water extractions as well as ion-selective microsensors. Porewater extractions revealed ecotoxicologically critical NO2(-) concentrations in hypoxic and anoxic sediment layers in which significant NO3(-) consumption took place. In contrast, the use of ion-selective microsensors demonstrated the high capacity of the thin oxic surface layer of the sediments to consume NO2(-) and to produce NO3(-). Two modes of NO3(-) supply to the sediments were compared: In treatments with NO3(-) supply to the overlying water, a subsurface maximum of NO2(-) concentration was observed, coinciding with the site of maximum NO3(-) consumption. When NO3(-) was perfused up through the sediment cores, however, NO2(-) accumulated throughout the entire sediment column. Such spatially extensive NO2(-) accumulations were only observed in sediments poor in organic matter with a relatively high permeability. By manipulating the O2 content of the overlying water, the release of NO2(-) from the sediments could be influenced: In treatments with air-saturated overlying water, the sediments did not release detectable amounts of NO2(-) into the water phase. When kept hypoxic (25% air saturation) instead, significant NO2(-) accumulations were recorded in the overlying water. These findings suggest that in treatments with air-saturated overlying water, NO2(-) that was produced in deeper sediment layers (denitrifying conditions) was completely consumed at the oxic sediment surface (nitrifying conditions) before it could reach the overlying water.     

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms

Background

History drives community assembly through differences both in density (density effects) and in the sequence in which species arrive (sequence effects). Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency) alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly.

Methods/Findings

We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.). Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition.

Conclusions

A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the “ingredients” (species) in ecological communities but their “recipes” as well.     

Development, maintenance and role of riparian vegetation in the river landscape

1. Riparian structure and function were considered from a longitudinal perspective in order to identify multiscale couplings with adjacent ecosystems and to identify research needs. 2. We characterized functional zones (with respect to vegetation development in association with various biogeochemical processes) within geomorphological settings using a delineation based upon erosional, transitional and depositional properties. 3. Vegetation dynamics within the riparian corridor are clearly influenced substantially by hydrological disturbance regimes. In turn, we suggest that vegetation productivity and diversity may widely influence riverine biogeochemical processes, especially as related to the consequences of changing redox conditions occurring from upstream to downstream. 4. However, surface and groundwater linkages are the predominant controls of landscape connectivity within riparian systems. 5. The importance of riparian zones as sources and sinks of matter and energy was examined in context of structural and functional attributes, such as sequestering or cycling of nutrients in sediments, retention of water in vegetation, and retention, diffusion or dispersal of biota. 6. The consequences of interactions between different communities (e.g. animals and plants, micro-organisms and plants) on biogeochemical processes are notably in need of research, especially with respect to control of landscape features. Multiscale approaches, coupling regional and local factors in all three spatial dimensions, are needed in order to understand more synthetically and to model biogeochemical and community processes within the river-riparian-upland landscape of catchments.