Local factors control the community composition of cyanobacteria in lakes while heterotrophic bacteria follow a neutral model

1. Neutral community models are derived from the proposition that basic probabilities of species loss (extinction, emigration) and gain (immigration, speciation) explain biological community structure, such that species with many individuals are very likely to be widespread. Niche models on the other hand assume that interactions between species and differential resource use mediate species coexistence, thus invoking environmental factors to explain community patterns. 2. In this study, we compared neutral and niche models to test how much of the spatial variability of assemblages of heterotrophic bacteria and phytoplankton in 13 lakes they could explain. Analysis of phytoplankton was restricted to cyanobacteria, so that they could be studied with the same molecular fingerprinting method, automated ribosomal intergenic spaces analysis (ARISA), as heterotrophic bacteria. We determined local biotic and abiotic lake variables as well as lake age, glacial history and distance between sites. 3. The neutral community model had a good fit to the community composition of heterotrophic bacteria (R² = 0.69), whereas it could not produce a significant model for the community composition of cyanobacteria. 4. The community composition of cyanobacteria was instead correlated to environmental variables. The best model, a combination of total organic carbon, biomass of eukaryotic phytoplankton, pH and conductivity, could explain 8% of the variation. In contrast, variation in the community composition of heterotrophic bacteria was not predicted by any of the environmental variables. Historical and spatial variables were not correlated to the community composition of either group. 5. The pattern found for heterotrophic bacteria suggests that stochastic processes are important. The correlation of cyanobacteria with local environmental variables alone is consistent with the niche model. We suggest that cyanobacteria, a group of organisms containing bloom‐forming species, may be less likely to fit a neutral community model, since these blooms are usually triggered by a particular combination of environmental conditions.     

Effect of sediment quality on benthic macroinvertebrate communities in streams in the north of France

The Nord/Pas-de-Calais region located in the North of France has been submitted, for several decades, to important pollution due to intensive industrialization. The present study reports on the effects of the metal and organic content of sediments in different streams on the benthic fauna, using multivariate analyses (PCA, CA, co-inertia analysis). Benthic macroinvertebrate communities present different assemblages along the Canal à Grand Gabarit and the river Aa, both in its natural and in its canalized stretches. These differences are more specifically due to anthropic factors such as the regulation of waterways and urban and industrial contamination. Co-inertia analysis enables to bring to the light the existence of a significant co-structure between environmental and faunistic data. This revised version was published online in September 2006 with corrections to the Cover Date.     

Seasonal and management influences on bacterial community structure in an upland grassland soil

Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.     

Combined monitoring of changes in δ13CH4 and archaeal community structure during mesophilic methanization of municipal solid waste

Reconstituted municipal solid waste (MSW) with varying contents of putrescible and cellulosic waste was incubated anaerobically under mesophilic conditions. Standard physicochemical parameters were monitored, together with stable isotopic signatures of produced CH₄ and CO₂. δ¹³C values for CH₄ indicated a change of methanogenic metabolism with time. CH₄ was predominantly produced from H₂/CO₂ at the beginning of the incubations. This period was associated with important shifts in archaeal communities monitored by automated ribosomal intergenic spacer analysis (ARISA) and FISH of oligonucleotidic probes targeting specifically 16S rRNA gene of various methanogenic groups. The onset of the active methane generation phase was characterized by an increase of CH₄δ¹³C, indicating a progressive shift toward an aceticlastic metabolism. When the methane production levelled off, a decrease in the isotopic signature was observed toward values characteristics of hydrogenotrophic metabolism. ARISA profiles were, however, found to be stable from the beginning of the active methane generation phase until the end of the experiment. FISH observation indicated that members of the family Methanosarcinaceae were predominant in the archaeal community during this period, suggesting that these methanogens might exhibit a high metabolic versatility during methanization of waste.     

Physiological indicators of fitness in benthic invertebrates: a useful measure for ecological health assessment and experimental ecology

Physiological indicators of fitness present a measure of an organism’s response to a changing environment. An analysis of how these organisms allocate and store their energy resources provides an understanding of how they cope with such environmental changes. Each individual has to balance the investment necessary to acquire a certain resource with the energy gained by it. This trade-off can be monitored by measuring several physiological indicators of fitness such as energy storage components, metabolic state or RNA/DNA ratio. Because environmental adaptations and ecological strategies of survival are best examined within the natural environment, our research has to rely on the physiological indicators that are easily accessible in the field. The physiological indicators presented here are significant for an individual’s fitness and in turn lead to reliable values in field-collected samples. Based on our own expertise and on a literature survey, the physiological relevance of the presented indicators is explained. Furthermore, some consideration to the analytical methods used to obtain the physiological indicators is given, and possible errors introduced at the sampling site and during the laboratory procedures are discussed. This work demonstrates that the integration of ecological and physiological expertise facilitates the identification of future ecological problems much earlier than separate approaches of both disciplines alone.     

Herbs and grasses as an allochthonous resource in open-canopy headwater streams

1. The organic matter dynamics of streams dominated by herbs and grass on their banks are poorly understood, despite the fact that such streams are common worldwide. Further, herbs and grasses can provide large quantities of detritus to stream food webs, and particularly small streams can be heavily shaded by overhanging vegetation, perhaps limiting in‐stream primary production. 2. We quantified the standing crop of edge vegetation and associated macroinvertebrate communities along three headwater streams with herbaceous and grass riparian vegetation on agricultural land in the Piedmont of Maryland, U.S.A., measured the decomposition of four common species of herbs and grasses using experimental leaf packs, and removed edge vegetation experimentally to determine the effect of shading on benthic algal production. 3. Large standing crops of plant material (average range: 68–276 g ash‐free dry mass per m⁻²), composed largely of monocotyledons, were found at all three study streams. These values are similar to those for coarse particulate organic matter in deciduous forested streams in the eastern U.S.A. In addition, diverse assemblages of shredding macroinvertebrates were observed at all three study sites. 4. Decomposition of the herbs was faster than that of the grasses, and both decomposed faster than most deciduous tree leaf litter. The decomposition rates of the herbs and grasses were significantly related to leaf quality as measured by leaf nitrogen content. Macroinvertebrate shredders colonized all experimental leaf packs, and the colonization of the herbs was faster than that of the grasses. 5. The accrual of chlorophyll‐a after the removal of shading vegetation was faster than that measured prior to removal as well as that in an unmanipulated control reach. 6. Given that the standing crop of organic matter in streams with herbs and grass along their banks was similar to that in forested streams, that the organic matter was rich in nitrogen and used by detritivores, and riparian shading limited algal growth, we suggest that herbaceous and grass plant material may be an important allochthonous food resource in such systems.     

Hindcasting cyanobacterial communities in Lake Okaro with germination experiments and genetic analyses

Cyanobacterial blooms are becoming increasingly prevalent worldwide. Sparse historic phytoplankton records often result in uncertainty as to whether bloom-forming species have always been present and are proliferating in response to eutrophication or climate change, or if there has been a succession of new arrivals through recent history. This study evaluated the relative efficacies of germination experiments and automated rRNA intergenic spacer analysis (ARISA) assays in identifying cyanobacteria in a sediment core and thus reconstructing the historical composition of cyanobacterial communities. A core (360 mm in depth) was taken in the central, undisturbed basin of Lake Okaro, New Zealand, a lake with a rapid advance of eutrophication and increasing cyanobacteria populations. The core incorporated a tephra from an 1886 volcanic eruption that served to delineate recent sediment deposition. ARISA and germination experiments successfully detected akinete-forming nostocaleans in sediment dating 120 bp and showed little change in Nostocales species structure over this time scale. Species that had not previously been documented in the lake were identified including Aphanizomenon issatschenkoi , a potent anatoxin-a producer. The historic composition of Chrococcales and Oscillatoriales was more difficult to reconstruct, potentially due to the relatively rapid degradation of vegetative cells within sediment.     

Conservation and variation of ribosomal DNA in eukaryotes

The organization of ribosomal DNA clusters, repetitive units, and their conserved and variable elements in eukaryotes is considered with special emphasis on the structure and function of the ribosomal intergenic spacer (rIGS). Data on rDNA variation, evolution, and possible role in various biological processes are reviewed.     

2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D.     

Relationships between stream acidity and bacteria,macroinvertebrates, and fish: a comparison of north temperate and south temperate mountain streams,USA

A comparative study of relationships between stream acidity and bacteria, macroinvertebrates, and fish in the Adirondack Mountains of upper New York state and in the Southern Blue Ridge Mountains of eastern Tennessee, USA, was conducted. Although the study sites in both regions spanned a pH range from approximately 4.5 to 6.4, considerably greater seasonal variability in pH and higher monomeric Al concentrations characterized the Adirondack sites. Relationships between several biological characteristics and stream water acidity were similar in both regions, including lower production of epilithic bacteria and bacteria on decomposing leaves, lower leaf decomposition rates, lower density and generic richness of scraper/grazer macroinvertebrates, particularly Ephemeroptera, and lower fish abundance and survival in more acidic streams. Densities of total macroinvertebrates and densities of macroinvertebrates and bacteria inhabiting or closely associated with stream sediments were generally not related to stream water acidity.Regional differences occur in some of the relationships between biological characteristics and stream water acidity. Negative correlations between bacterial production on rocks and pH, between bacterial production on decomposing leaves and pH, and between densities of Ephemeroptera and scrapers and pH were stronger in the Adirondacks than in the Southern Blue Ridge. Higher Al concentrations in the Adirondacks may be responsible for the stronger relationships with pH there. The steeper slopes of the relationships between Ephemeroptera density and all forms of Al in the Adirondacks compared with the Southern Blue Ridge suggests that there may be some adaptation among a few acid/aluminum-tolerant species in the seasonally more constant acidic Southern Blue Ridge streams. Fish bioassays indicated longer survival times in acidic streams in the Adirondacks compared with the Southern Blue Ridge, but these results may be an artifact associated with the use in the Southern Blue Ridge of rainbow trout as the test species which is known to be more acid sensitive compared with brook trout, the test species used in the Adirondacks.     

A comparison of clustering methods for river benthic community analysis

Four commonly used clustering methods (UPGMA, Ward Linkage,Complete Linkage and TWINSPAN) were compared in their abilitytorecognise the structure of three river macroinvertebratesdatasetswhich were pre-determined based on habitat and biologicalcharacteristics or chemical water quality of sampling sites.DCA,NMDS and ANOSIM were applied to the same datasets to providefurther information about data structure, and nonparametrictestswere also undertaken on major chemical variables to justifythepredeterminations. The modified Rand Index was used to measuretheagreement between a particular solution and the pre-determinedclassification. The results showed that Ward Linkage performedbestwhen its use was broadened and used with the CY DissimilarityMeasure, followed by TWINSPAN and Complete Linkage with UPGMAbeingleast successful. There was evidence to suggest that theeffectiveness of some clustering methods (e.g. UPGMA) may varyatdifferent clustering levels, and simulation techniques whichhavebeen used to assess clustering methods could leave somepropertiesof clustering methods unexamined.     

Predictability of streamflow and particulate organic matter concentration as indicators of stability in prairie streams

Predictability of stream discharge and particulate organic matter (POM) in the water column was estimated, using Colwell's indices of constancy and contingency, for 6 Texas prairie streams (1 each of 2nd, 3rd, and 4th order with intermittent or perennial discharge). Stream discharge in these 6 prairie streams varied between 0 and 36000 1 s^–1, depending on the stream and season. Predictability (P) of discharge in these streams ranged from 0.45 to 0.62, within the range of values expected for North American streams. Predictability of stream discharge was not significantly different between streams. Particulate organic matter concentrations in these prairie streams are relatively low, ranging from 0.25 to 4.00 mg AFDM 1^–1. Predictability of POM concentration in these streams was high, ranging from 0.75 to 0.85, and was largely the result of constancy of POM concentrations. Within the different POM size classes, Fine POM (FPOM) had the highest predictability (P = 0.89–0.96). In spite of relatively unpredictable stream discharge, POM remained fairly constant providing a measure of habitat predictability and stability.     

A comparison of bacterial,ciliate and macroinvertebrate indicators of stream ecological health

We evaluate the reliability of communities of bacteria and ciliated protozoa as indicators of freshwater ecological health. Samples of epilithic biofilm were taken from 18 freshwater streams, impacted by varying types and degrees of catchment modification. Communities of bacteria and ciliates were characterised using DNA fingerprinting techniques (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism, respectively) and macroinvertebrate data also obtained, for comparison. Similar to the macroinvertebrates, the taxa richness of ciliate communities was reduced in more developed stream catchments; significant differences in the evenness of ciliate communities were also detected. We could identify no significant relationship between the richness of bacterial taxa and the percentage catchment development. However, a significant trend was detected between bacterial community structure and the predominant catchment land use (rural vs. urban) using a Bray–Curtis measure of similarity, a relationship not detected for the ciliate and macroinvertebrate communities. These findings indicate that stream bacterial, ciliate and macroinvertebrate communities each respond differently to various catchment conditions and highlight the potential of microbial communities to provide novel, alternative indicators of stream ecosystem health.     

Impact of arsenic and antimony contamination on benthic invertebrates in a minor Corsican river

The chemical and biological characteristics of a Corsican river that drains contaminated waters and sediment from an abandoned realgar mine were studied. The concentrations of pollutants such as As and Sb were found to be notably high. For example, in the Presa River, downstream the realgar mine, the mean As concentrations in the water and in the sediment were 3010 g 1^-1 and 9450 g g^-1 respectively. Species richness and abundance of benthic invertebrates decreased downstream the As mine. The disappearance of oligochaetes, leeches and a rarity of mayfly populations have been evidenced. On the contrary, a large increase in species belonging to stoneflies and gastropods was found. Some species like Baetis cyrneus, Ephemerella ignita, Sericostoma clypeatum and Ibisia marginata were more sensitive to As and Sb concentrations while others species like Ancylus fluviatilis, Isoperla insularis, Hydropsyche cyrnotica, Caenis luctuosa and Silonella aurata were less sensitive. The benthic invertebrates show different reactions in this contaminated environment, which could be explained by their feeding behaviours and certain morphological characteristics.     

Modification of benthic insect communities in polluted streams: combined effects of sedimentation and nutrient enrichment

Responses of the benthic insect community of a southern Appalachian trout stream to inorganic sedimentation and nutrient enrichment were monitored over a period of eight months. Entry of pollutants from point sources established differentially polluted zones, allowing an assessment of impacts due to sedimentation alone and in association with elevated nutrient levels. Input of sediment resulted in a significant increase in bed load and decrease of pH at the substrate-water interface (P < 0.05). The zone receiving nutrient runoff from livestock pasture exhibited elevated levels of nitrate and phosphate, but available data indicated such concentrations to be quite low. Species richness, diversity, and total biomass of filter feeding Trichoptera and Diptera, predaceous Plecoptera, and certain Ephemeroptera were significantly reduced in the polluted zones. Inorganic sedimentation, operating indirectly through disruption of feeding and filling of interstitial spaces, was considered to be the primary factor affecting filter feeding taxa. Decomposition of compounds associated with materials in the bed load may depress pH and eliminate acid sensitive species of Plecoptera and Ephemeroptera. Such processes of acidification may be particularly important to Appalachian streams since the pH of regional surface waters is characteristically acidic prior to sedimentation. Accumulation of particles on body surfaces and respiratory structures, perhaps as a function of wax and mucous secretion or surface electrical properties, appears to be the major direct effect of inorganic sedimentation on stream insects. Growths of the filamentous bacterium Sphaerotilus natans were also frequently associated with silted individuals in the zone receiving nutrient addition. Distribution of the bacterium suggested that silted substrates, perhaps as related to the presence of iron compounds, are required for colonization in dilute nutrient solutions. The primary effect of Sphaerotilus colonies appears to be augmentation of particle accumulation through net formation by bacterial filaments. Data indicate that inorganic sedimentation and nutrient addition operate synergistically, eliminating a significantly greater number of taxa than exposure to one pollutant alone.     

Genetic variability in intergenic spacers of ribosomal DNA in Pisolithus isolates associated with pine, eucalyptus and Afzelia in lowland Kenyan forests

Basidiocarps of Pisolithus associated with indigenous ( Afzelia quanzensis Welw.) and introduced ( Pinus caribaea Mor. and Eucalyptus camaldulensis Dehnh.) hosts in the lowland forests of the Coast Province of Kenya are morphologically distinct. Genetic variability among 52 Pisolithus basidiocarps, collected beneath the various host plants, was examined based on sequence polymorphism within the internal transcribed spacer (ITS) and intergenic spacer (IGS1) of ribosomal DNA genes. Variability in ITS and IGS1 sequences indicated that the three host-associated morphotypes were genetically different. Consensus trees generated by bootstrap analysis of sequence data of Pisolithus isolates from Australia and Kenya are polyphyletic and strongly suggest that the three different morphotypes/genotypes present in Kenya represent separate biological species. In addition, our data indicate that little genetic exchange occurs in silva between these species.     

Spatial and temporal heterogeneity of the bacterial communities in stream epilithic biofilms

The spatial and temporal variability in bacterial communities within freshwater systems is poorly understood. The bacterial composition of stream epilithic biofilms across a range of different spatial and temporal scales both within and between streams and across the profile of individual stream rocks was characterised using a community DNA-fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA). The differences in bacterial community structure between two different streams were found to be greater than the spatial variability within each stream site, and were larger than the weekly temporal variation measured over a 10-week study period. Greater variations in bacterial community profiles were detected on different faces of individual stream rocks than between whole rocks sampled within a 9-m stream section. Stream temperature was found to be the most important determinant of bacterial community variability using distance-based redundancy analysis (dbRDA) of ARISA data, which may have broad implications for riparian zone management and ecological change as a consequence of global warming. The combination of ARISA with multivariate statistical methods and ordination, such as multidimensional scaling (MDS), permutational manova and RDA, provided rapid and effective methods for quantifying and visualising variation in bacterial community structure, and to identify potential drivers of ecological change.     

The quantification of local substrate heterogeneity in streams and its significance for macroinvertebrate assemblages

The effect of substrate heterogeneity on the structure of stream macroinvertebrate assemblages (total abundance, taxon richness, and evenness) is still not clear, but this could be due to the lack of standard methods for quantifying substrate heterogeneity. An accurate quantification of substrate heterogeneity was obtained from photographs of sampled areas (each 225 cm²), which were used to create maps that were subsequently digitized and analyzed using image analysis software. These maps allowed the calculation of multiple metrics quantifying two aspects of substrate heterogeneity: composition and spatial configuration of substrate patches. The diversity of substrate types (calculated as the Shannon diversity index), and the heterogeneity of patch compactness (calculated as the coefficient of variation of the relationship between patch dimensions) were the metrics explaining more biotic variance at the sample scale, but at higher scales there were no relationships between assemblage structure and substrate heterogeneity. Most variation in substrate heterogeneity occurred at the sample scale, while some metrics varied significantly at riffle or segment scales; these patterns of variation match those of macroinvertebrate assemblages, which had been previously studied. The importance of quantifying substrate heterogeneity and considering the spatial scales of its study are discussed.