Relationships between structure and function in streams contrasting in temperature

1. We studied 10 first-order Icelandic streams differing in geothermal influence in separate catchments. Summer temperature (August–September) ranged between 6 and 23 °C.
2. Macroinvertebrate evenness and species overlap decreased significantly with temperature whereas taxon richness showed no response. In total, 35 macroinvertebrate species were found with Chironomidae the dominant taxonomic group. Macroinvertebrate density increased significantly with temperature. Dominant species in the warm streams were Lymnaea peregra and Simulium vittatum . Algal biomass, macrophyte cover and richness were unrelated to temperature. Densities of trout ( Salmo trutta ), the only fish species present, reflected habitat conditions and to a lesser degree temperature.
3. Density of filter-feeders increased significantly with temperature whereas scraper density, the other dominant functional feeding group, was unrelated to temperature. Stable isotope analysis revealed a positive relationship between δ¹⁵N and temperature across several trophic levels. No pattern was found with regard to δ¹³C and temperature.
4. Leaf litter decomposition in both fine and coarse mesh leaf bags were significantly correlated to temperature. In coarse mesh leaf packs breakdown rates were almost doubled compared with fine mesh, ranging between 0.5 and 1.3 g DW 28 days⁻¹. Nutrient diffusion substrates showed that the streams were primarily nitrogen limited across the temperature gradient while a significant additional effect of phosphorous was found with increasing temperature.
5. Structural and functional attributes gave complementary information which all indicated a change with temperature similar to what is found in moderately polluted streams. Our results therefore suggest that lotic ecosystems could be degraded by global warming.     

Competition between ammonia-oxidizing bacteria and benthic microalgae

The abundance, activity, and diversity of ammonia-oxidizing bacteria (AOB) were studied in prepared microcosms with and without microphytobenthic activity. In the microcosm without alga activity, both AOB abundance, estimated by real-time PCR, and potential nitrification increased during the course of the experiment. AOB present in the oxic zone of these sediments were able to fully exploit their nitrification potential because NH(4)(+) did not limit growth. In contrast, AOB in the alga-colonized sediments reached less than 20% of their potential activity, suggesting starvation of cells. Starvation resulted in a decrease with time in the abundance of AOB as well as in nitrification potential. This decrease was correlated with an increase in alga biomass, suggesting competitive exclusion of AOB by microalgae. Induction of N limitation in the oxic zone of the alga-colonized sediments and O(2) limitation of the majority of AOB in darkness were major mechanisms by which microalgae suppressed the growth and survival of AOB. The competition pressure from the algae seemed to act on the entire population of AOB, as no differences were observed by denaturing gradient gel electrophoresis of amoA fragments during the course of the experiment. Enumeration of bacteria based on 16S rRNA gene copies and d-amino acids suggested that the algae also affected other bacterial groups negatively. Our data indicate that direct competitive interaction takes place between algae and AOB and that benthic algae are superior competitors because they have higher N uptake rates and grow faster than AOB.     

Nutrition and physiology of denitrifying bacteria

Summary The size of both the denitrifying and the total bacterial population was found to be positively correlated with soil pH, but the denitrifying bacteria were more sensitive to acid environments than the bacterial microflora as a whole. The ecological evidence for a pH effect was supported by studies with individual pure cultures. The estimate of abundance of denitrifying micro-organisms was also affected markedly by the composition of the medium, and an improved medium has been proposed.Marked differences were noted in the nutrition of the bacteria capable of N₂ production. In the absence of oxygen, certain strains developed readily using nitrate as the terminal electron acceptor for growth in media with no preformed growth factors, but others required ammonium or growth factors for denitrification to occur.The investigation was supported in part by funds provided by the Sun Oil Company and Cooperative Regional Research Project NE-39. Present address of senior author: Department of Soils, College of Agriculture, University of Phillippines. A gronomy Paper No. 528.     

Diversity of culturable denitrifying bacteria

Sequence divergence in the ribosomal genes of known strains and isolates of aquatic denitrifying bacteria was investigated using restriction fragment length polymorphism (RFLP) analysis. The same cultures were characterized for their homology with antibody and gene probes for nitrite reductase (NiR), a key enzyme in the denitrification pathway, and for amplification with a set of polymerase chain reaction primers designed to amplify a portion of the NiR gene. The NiR probes were developed from Pseudomonas stutzeri (ATCC 14405) and several P. stutzeri strains were included in the analyses. The RFLP analysis clustered most of the P. stutzeri strains together, but detected considerable diversity within this group. Isolates from three aquatic environments exhibited within —and among — habitat diversity by RFLP. Hybridization with the NiR probes and amplification with the NiR primers were not correlated with the clustering of strains by rDNA RFLP analysis. The relationships among strains deduced from ribosomal DNA RFLP reflect heterogeneity within the P. stutzeri group and among other pseudomonads, and the patterns differ from those inferred from specificity of the NiR probes.Abbreviations NiR Nitrite reductase - PCR polymerase chain reaction - RFLP restriction fragment length polymorphism     

Untangling associations between chironomid taxa in Neotropical streams using local and landscape filters

1. Analyses of species association have major implications for selecting indicators for freshwater biomonitoring and conservation, because they allow for the elimination of redundant information and focus on taxa that can be easily handled and identified. These analyses are particularly relevant in the debate about using speciose groups (such as the Chironomidae) as indicators in the tropics, because they require difficult and time‐consuming analysis, and their responses to environmental gradients, including anthropogenic stressors, are poorly known. 2. Our objective was to show whether chironomid assemblages in Neotropical streams include clear associations of taxa and, if so, how well these associations could be explained by a set of models containing information from different spatial scales. For this, we formulated a priori models that allowed for the influence of local, landscape and spatial factors on chironomid taxon associations (CTA). These models represented biological hypotheses capable of explaining associations between chironomid taxa. For instance, CTA could be best explained by local variables (e.g. pH, conductivity and water temperature) or by processes acting at wider landscape scales (e.g. percentage of forest cover). 3. Biological data were taken from 61 streams in Southeastern Brazil, 47 of which were in well‐preserved regions, and 14 of which drained areas severely affected by anthropogenic activities. We adopted a model selection procedure using Akaike’s information criterion to determine the most parsimonious models for explaining CTA. 4. Applying Kendall’s coefficient of concordance, seven genera (Tanytarsus/Caladomyia, Ablabesmyia, Parametriocnemus, Pentaneura, Nanocladius, Polypedilum and Rheotanytarsus) were identified as associated taxa. The best‐supported model explained 42.6% of the total variance in the abundance of associated taxa. This model combined local and landscape environmental filters and spatial variables (which were derived from eigenfunction analysis). However, the model with local filters and spatial variables also had a good chance of being selected as the best model. 5. Standardised partial regression coefficients of local and landscape filters, including spatial variables, derived from model averaging allowed an estimation of which variables were best correlated with the abundance of associated taxa. In general, the abundance of the associated genera tended to be lower in streams characterised by a high percentage of forest cover (landscape scale), lower proportion of muddy substrata and high values of pH and conductivity (local scale). 6. Overall, our main result adds to the increasing number of studies that have indicated the importance of local and landscape variables, as well as the spatial relationships among sampling sites, for explaining aquatic insect community patterns in streams. Furthermore, our findings open new possibilities for the elimination of redundant data in the assessment of anthropogenic impacts on tropical streams.     

Nitrifying and denitrifying pathways of methanotrophic bacteria

Nitrous oxide, a potent greenhouse gas and ozone-depleting molecule, continues to accumulate in the atmosphere as a product of anthropogenic activities and land-use change. Nitrogen oxides are intermediates of nitrification and denitrification and are released as terminal products under conditions such as high nitrogen load and low oxygen tension among other factors. The rapid completion and public availability of microbial genome sequences has revealed a high level of enzymatic redundancy in pathways terminating in nitrogen oxide metabolites, with few enzymes involved in returning nitrogen oxides to dinitrogen. The aerobic methanotrophic bacteria are particularly useful for discovering and analysing diverse mechanisms for nitrogen oxide production, as these microbes both nitrify (oxidize ammonia to nitrite) and denitrify (reduce nitrate/nitrite to nitrous oxide via nitric oxide), and yet do not rely on these pathways for growth. The fact that methanotrophs have a rich inventory for nitrogen oxide metabolism is, in part, a consequence of their evolutionary relatedness to ammonia-oxidizing bacteria. Furthermore, the ability of individual methanotrophic taxa to resist toxic intermediates of nitrogen metabolism affects the relative abundance of nitrogen oxides released into the environment, the composition of their community, and the balance between nitrogen and methane cycling.     

The physiological genetics of denitrifying bacteria

The genetics of denitrification is a relatively unexplored area that has great promise. Species of Pseudomonas are probably best suited for study because they are widely found among natural denitrifying populations and are quite readily amenable to genetic analysis. The techniques for mutagenesis and for the exchange of chromosomal genes to characterize mutant strains have been well-developed in P. aeruginosa and are being developed in P. stutzeri. Mutants defective in the denitrification of nitrate, nitrite, and nitrous oxide are now available and will aid in describing the catalytic and regulatory elements of the denitrification pathway.     

Relationships between the isotopic composition of dissolved organic carbon and its bioavailability in contrasting Ozark streams

Bioavailability of dissolved organic carbon (DOC) can significantly influence nutrient cycling in small streams yet the factors influencing the bioavailability of DOC remains poorly understood. The isotopic composition of DOC and factors controlling its utilization were studied in two contrasting headwater streams to elucidate the relationship between DOC source and its bioavailability. Water samples were collected monthly from Moore Creek (MC), located in a watershed dominated by fertilized pasture, and from Huey Hollow (HH), located in a deciduous forest watershed. Dissolved organic carbon concentrations ranged from 222 to 1130 μm C and 35 to 289 μm C in MC and HH, respectively. The isotopic composition of DOC (δ¹³C_DOC) was more seasonally variable in HH and ranged from ?33.6 to ?28.0?, as compared with MC where it ranged from ?27.2 to ?24.5 ?. The δ¹³C_DOC in Huey Hollow suggests leaf debris was an important source of DOC throughout most of the year while algae was important in winter and early spring. In MC, the δ¹³C_DOC indicated DOC was largely derived from soil organic matter while algal inputs were small relative to the large pool of refractory DOC. Stream water community respiration (SWCR) rates suggest the existence of a larger pool of refractory DOC in MC relative to HH. The ratio of SWCR (μM C h^?1) to DOC concentration (mM C) was generally higher in HH (1.2–13.2) as compared with MC (0.2–4.2), suggesting that relative bioavailability of DOC was often greater in HH. Nutrient addition experiments indicate that bioavailable C limited SWCR in spring and fall in MC, while bioavailable C was never limiting in HH. The results suggest that elevated nutrient and DOC concentrations supported higher levels of microbial activity that resulted in a large pool of refractory DOC in MC. The lower inorganic nutrient and DOC concentrations reduced microbial activity in HH and likely limited the production of refractory DOC. Results of this study suggest that both organic matter source and nutrient concentration are important determinants of DOC bioavailability in small streams. %     

Analysis of denitrifying communities in streams from an urban and non-urban catchment

Urbanization leads to degradation in water quality and has a major effect on the biota of streams, but its effect on microbial communities is not as well understood. DNA-techniques that target functional genes are being used to examine microbial communities, but less frequently applied to freshwater aquatic systems. Our aim was to determine whether terminal restriction fragment length polymorphism and sequence analysis of polymerase chain reaction-amplified (PCR) nosZ gene sequences could be used to show if there were measurable differences in the denitrifying community in two urban streams in catchments with contrasting degrees of catchment urbanization. Community structure in the sediments and associated riparian zones were studied at the contrasting sites. We showed that the denitrifying community in the sediments and riparian soils of the two streams were significantly different. There were also significant differences between the sediment and riparian zone communities within each of the sites. Terminal restriction fragment length polymorphism analysis proved to be a valuable technique that could resolve patterns of the denitrifying community in streams of contrasting degrees of urbanization, but sequence analysis was required to confirm the identity of the amplified products.     

The physiological genetics of denitrifying bacteria

The genetics of denitrification is a relatively unexplored area that has great promise. Species of Pseudomonas are probably best suited for study because they are widely found among natural denitrifying populations and are quite readily amenable to genetic analysis. The techniques for mutagenesis and for the exchange of chromosomal genes to characterize mutant strains have been well-developed in P. aeruginosa and are being developed in P. stutzeri. Mutants defective in the denitrification of nitrate, nitrite, and nitrous oxide are now available and will aid in describing the catalytic and regulatory elements of the denitrification pathway.     

Metabolism of nitric oxide in soil and denitrifying bacteria

Abstract Production and consumption of NO was measured under anaerobic conditions in a slightly alkaline and an acidic soil as well as in pure cultures of denitrifying Pseudomonas aeruginosa, P. stutzeri, P. fluorescens, Paracoccus denitrificans, Azospirillum brasilense , and A. lipoferum . Growing bacterial cultures reduced nitrate and intermediately accumulated nitrite, NO, N₂O, but not NO₂. Addition of formaldehyde inhibited NO production and NO consumption. In the presence of acetylene NO was reduced to N₂O. Net NO release rates in denitrifying bacterial suspensions and in soil samples decreased hyperbolically with increasing NO up to mixing ratios of about 5 ppmv NO. This behaviour could be modelled by assuming a constant rate of NO production simultaneously with a NO consumption activity that increased with NO until V _max was reached. The data allowed calculation of the gross rates ( P ) of NO production, of the rate constants ( k ), V _max and K _m of NO consumption, and of the NO compensation mixing ratio ( m _c). In soil, P was larger than V _max resulting in net NO release even at high NO mixing ratios unless P was selectively inhibited by chlorate + chlorite or by aerobic incubation conditions. In bacteria, V _max was somewhat larger than P resulting in net NO uptake at high NO mixing ratios. Both P and V _max were dependent on the supply of electron donor (e.g. glucose). Both in soil (aerobic or anaerobic) and in pure culture, the K _m values of NO consumption were in a similar low range of about 0.5–6.0 nM. Anaerobic soil and denitrifying bacteria exhibited m _c values of 1.6–2.1 ppmv NO and 0.2–4.0 ppmv NO, respectively.     

Development and application of a novel and effective screening method for aerobic denitrifying bacteria

Herein we describe a novel and effective screening method for aerobic denitrifying bacteria. For this procedure, we utilized KCN to inhibit the electron transference from Cytaa3 to oxygen in the bacteria respiratory chain. We employed a 3-h aeration operation cycle and intermittent rotations. The resultant bacterial suspensions were plated on a KCN-screening medium and incubated aerobically. Single colonies were selected and incubated in an aerobic culture medium. Culture nitrate and nitrite levels were determined over time, and ultimately four bacterial strains that performed denitrifying under aerobic conditions were identified by this method. Of these, strain Y2-1-1 demonstrated the best aerobic denitrifying ability. In a 5-day test, the NO3--N of the aerobic culture medium was reduced from 282.0+/-8.3 mg L(-1) to 149.2+/-17.1 mg L(-1), with little nitrite or N2O production. The morphological, physiological and biochemical characteristics and the 16S rRNA gene sequence homology comparison data for this strain were consistent with the classification of the genus Pseudomonas. We named this strain Pseudomonas sp. Y2-1-1.     

Ecophysiology of abundant denitrifying bacteria in activated sludge

The abundance of potential denitrifiers in full-scale wastewater treatment plants with biological nitrogen and phosphorus removal was investigated by FISH and various oligonucleotide probes. The potential denitrifiers were characterized as probe-defined populations that were able to consume radiolabelled substrate with oxygen, nitrate and nitrite as electron acceptor as determined by microautoradiography. The most abundant potential denitrifiers were related to the genera Aquaspirillum, Azoarcus, Thauera and Rhodocyclus, all within the Betaproteobacteria. They made up 20-49% of all bacteria in most of the 17 nitrogen removal plants investigated and were hardly present in four plants without denitrification. The ecophysiology of Aquaspirillum, Azoarcus and Thauera-related bacteria was consistent within each probe-defined group in the plants investigated. These three groups showed distinct physiological differences, with the Aquaspirillum-related bacteria appearing as the most specialized one, consuming only amino acids among the substrates tested, and Thauera as the most versatile consuming some volatile fatty acids, ethanol and amino acids. The coexistence of Aquaspirillum, Azoarcus and Thauera-related bacteria in a range of treatment plants with differences in wastewater, design and operation suggest that the populations ensure a functional stability of the plants by occupying different ecological niches related to the carbon transformation.     

Taxonomy of denitrifying bacteria in soddy podzolic soil

The taxonomic composition of denitrifying bacteria in soddy podzolic soil was studied by the succession analysis method. This method revealed a significant variation in the taxonomic composition of denitrifying microorganisms in the course of succession. In contrast to succession analysis, the single microbiological analysis of soil samples reflected only the late stage of succession and thus led to an underestimation of the major members of succession. Myxobacteria were found to be the most active denitrifiers at the early stages of succession, whereas bacilli dominated at its late stages. The bacilli were represented by three facultatively anaerobic species, Bacillus cereus, Bac. circulans, and Bac. polymyxa.     

Anaerobic metabolism of cyclohexanol by denitrifying bacteria

Three strains of denitrifying bacteria were anaerobically enriched and isolated from oxic or anoxic habitats with cyclohexanol or cyclohexanone as sole electron donor and carbon source and with nitrate as electron acceptor. The bacteria were facultatively anaerobic, Gramnegative and metabolism was strictly oxidative with molecular oxygen, nitrate, or nitrite as terminal electron acceptor. Cyclohexanol and cyclohexanone were degraded both anaerobically and aerobically. Aromatic compounds were oxidized in the presence of molecular oxygen only. One of the bacterial strains was further characterized. During anaerobic cyclohexanol degradation approximately 40% of the substrate was oxidized to phenol, which accumulated as dead-endproduct in the growth medium; 60% of cyclohexanol was completely oxidized to CO₂ and assimilated, respectively. In addition to phenol formation, transient accumulation of cyclohexanone, 2-cyclohexenone and 1,3-cyclohexanedione was observed. Based on these findings we propose a pathway for anaerobic cyclohexanol degradation involving these intermediates.     

Aerobic and anaerobic growth of rifampin-resistant denitrifying bacteria in soil

The growth and survival of several rifampin-resistant isolates of denitrifying bacteria were examined under anaerobic (denitrifying) and aerobic conditions. Two isolates added to nonsterile Bruno soil at densities of between 10(4) and 10(6) CFU g dry soil-1 exhibited an initial period of growth followed by a gradual decline in numbers. After 28 days, both isolates maintained viable populations of between 10(4) and 10(5) CFU g dry soil-1 under both denitrifying and aerobic conditions. One of the isolates consistently grew better under denitrifying conditions, and the other isolate consistently grew better under aerobic conditions. The relative pattern of denitrifying versus aerobic growth for each organism was not affected by the addition of glucose. The growth yields of the two isolates varied with soil type, but the relative pattern of denitrifying versus aerobic growth was consistent in three soils with greatly different properties. Five of nine isolates introduced into Bruno soil at low population densities (approximately 10(5) CFU g dry soil-1) exhibited better growth after 2 days under denitrifying conditions. It was not possible to predict the prevalence of the denitrifying or aerobic mode of growth in nonsterile soil from the growth characteristics of the isolates in pure cultures or sterile soil.     

Contrasting effects of anthropogenic and natural acidity in streams: a meta-analysis

Large-scale human activities including the extensive combustion of fossil fuels have caused acidification of freshwater systems on a continental scale, resulting in reduced species diversity and, in some instances, impaired ecological functioning. In regions where acidity is natural, however, species diversity and functioning seem to be less affected. This contrasting response is likely to have more than one explanation including the possibility of adaptation in organisms exposed to natural acidity over evolutionary time scales and differential toxicity due to dissimilarities in water chemistry other than pH. However, empirical evidence supporting these hypotheses is equivocal. Partly, this is because previous research has mainly been conducted at relatively small geographical scales, and information on ecological functioning in this context is generally scarce. Our goal was to test whether anthropogenic acidity has stronger negative effects on species diversity and ecological functioning than natural acidity. Using a meta-analytic approach based on 60 datasets, we show that macroinvertebrate species richness and the decomposition of leaf litter -- an important process in small streams -- tend to decrease with increasing acidity across regions and across both the acidity categories. Macroinvertebrate species richness, however, declines three times more rapidly with increasing acidity where it is anthropogenic than where it is natural, in agreement with the adaptation hypothesis and the hypothesis of differences in water chemistry. By contrast, the loss in ecological functioning differs little between the categories, probably because increases in the biomass of taxa remaining at low pH compensate for losses in functionality that would otherwise accompany losses of taxa from acidic systems. This example from freshwater acidification illustrates how natural and anthropogenic stressors can differ markedly in their effects on species diversity and one aspect of ecological functioning.     

Common trends in mutualism revealed by model associations between invertebrates and bacteria

Mutually beneficial interactions between microorganisms and animals are a conserved and ubiquitous feature of biotic systems. In many instances animals, including humans, are dependent on their microbial associates for nutrition, defense, or development. To maintain these vital relationships, animals have evolved processes that ensure faithful transmission of specific microbial symbionts between generations. Elucidating mechanisms of transmission and symbiont specificity has been aided by the study of experimentally tractable invertebrate animals with diverse and highly evolved associations with microorganisms. Here, we review several invertebrate model systems that contribute to our current understanding of symbiont transmission, recognition, and specificity. Although the details of transmission and symbiont selection vary among associations, comparisons of diverse mutualistic associations are revealing a number of common themes, including restriction of symbiont diversity during transmission and glycan–lectin interactions during partner selection and recruitment.     

Substratum associations of benthic invertebrates in lowland and mountain streams

The preferences of aquatic invertebrate species for specific substrata at the river bottom have been subject of many studies. Several authors classified the substratum preferences of species or higher taxonomic units. Most of these compilations, however, are based on literature analyses and expert knowledge as opposed to the analysis of original data. To enhance our knowledge of invertebrate substratum preferences, we applied a ‘Multi-level pattern’ analysis based on almost 1000 substrate-specific invertebrate samples. The samples were taken in 18 streams in Germany, the Netherlands and Austria, comprising a total of 40 sampling sites and equally covering lowland and mountain streams. The main objectives of our analysis were (I) to derive substratum preferences of taxa in lowland and mountain streams, (II) to compare the preferences with existing data and (III) to compare species substratum associations between lowland and mountain streams. Of the 290 taxa analyzed, 188 were associated significantly to specific substrata. Twenty-five taxa in lowland streams and 51 taxa in mountain streams prefer one or two substratum types (of nine substratum types considered in total). In contrast, 112 species (mountain streams n = 84, lowland streams n = 28) are associated significantly with a broader range of substrata. We compared the classifications derived from our data analysis with those provided in the freshwaterecology.info database (www.freshwaterecology.info). Our results support the existing classifications of substratum preferences in most cases (70%). For 25 species, substratum preferences for both lowland and mountain streams were derived, many of them indicating different substratum associations in the two stream groups. As substratum preferences differed between closely related species, preferences should always be given at the species level as opposed to coarser taxonomic units.