RNA/DNA ratio as a growth indicator of stream periphyton

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Bacteria and algae in stream periphyton along a nutrient gradient

1. Stream riffles in southern Ontario and western Quèbec were sampled for biomass (58 stations from 51 streams) and production (22 stations from 21 streams) of algae and bacteria in periphyton to test the hypothesis that bacteria in benthic biofilms compete with algae for nutrients. 2. Algal and bacterial biomass were positively correlated, as were algal and bacterial production. Bacterial production was also positively correlated to algal and bacterial biomass, but the relationship was not significant. The ratio of algal to bacterial biomass did not vary with nutrients whereas algal production tended to increase with nutrients more rapidly than bacterial production. 3. Instream nitrogen concentrations explained 38–58% of the variability in algal biomass and production. Bacterial abundance explained an additional 9–29% of the residual variance in algal production and biomass. However, the relationship between bacterial abundance and algal production and biomass, once nutrients were taken into account, was positive, in contrast to the predicted effect of competition. 4. Hence, we reject our original hypothesis that bacteria in biofilms compete with algae for nutrients and instead suggest that bacteria and algae in biofilms coexist in an association that offers space and resources to sustain production of both groups of organisms.     

Vesicular-arbuscular mycorrhizal inoculum potential affects the growth of Stryphnodendron microstachyum seedlings in a Costa Rican human tropical lowland

This study used a plant bioassay to investigate the vesicular-arbuscular mycorrhizal (VAM) inoculum potential of soil from three vegetation types (fern, secondary forest, and grass) in an abandoned pasture in the tropical humid lowlands at La Selva, in northeastern Costa Rica. Growth, measured as seedling height, number of leaves, and total (above- and belowground) biomass, of Stryphnodendron microstachyum Poepp. et Endl. (Synon. S. excelsum Harms) seedlings was significantly lower when grown in soil inoculum from the fern areas than in soil inoculum from the forest and grass areas. However, S. microstachyum seedlings grown in the fern inoculum had significantly greater VAM colonization than seedlings grown in the forest and grass inoculum. In addition, roots collected from a dominant plant species from each of the three vegetation types showed that the fern (Nephrolepsis biserrata) had significantly greater mycorrhizal colonization than the tree (Pentaclethra macroloba (Willd.) Kuntze or the grass (Brachiaria spp.). The results of this study suggest that differences in mycorrhizal inoculum potential among vegetation types and its effects on seedling growth may have important implications for the restoration and management of degraded lands.     

Relationships between phytoplankton and periphyton communities in a central Iowa stream

Relationships between phytoplankton and periphyton communities were investigated in a central Iowa stream. Results generally support the hypothesis that the phytoplankton community arises from the epipelic periphyton community. A high correlation existed between the proportion of benthic diatoms composing the epipelon and phytoplankton. One dominant epipelic species (Nitzschia acicularis) showed a greater tendency to become planktonic than the grouped remainder of Nitzschia spp. There was a significant inverse relationship between the proportion of centric diatoms in the plankton and volume of flow. Centric diatoms were important members of the plankton only when volume of flow was less than 60 ft³ / sec (2.1 m³ / sec). Possible mechanisms explaining these phenomena are discussed.This study represents a portion of a dissertation submitted to the Graduate College, Iowa State University in partial fulfillment of requirements for the degree Doctor of Philosophy.     

Changes in atrazine toxicity throughout succession of stream periphyton communities

A study was made to describe atrazine toxicity and its changes throughout succession of periphyton communities of an undisturbed Mediterranean stream. Toxicity was assessed by short-term physiological tests (concentration-effect curves of photosynthesis to atrazine) in the laboratory using artificial substrates colonized in one stream site during winter, and two stream sites (one open and the other shaded) during summer. In the winter experiment, when environmental conditions were relatively steady and chlorophyll content was low, toxicity increased according to the increases in cell density and chlorophyll content throughout colonization. EC₅₀ (concentration inhibiting photosynthesis by 50%) was above 0.8 μM atrazine until day 16 and below 0.4 μM atrazine after three weeks. In the summer experiment, under more variable environmental conditions, the differences between the EC₅₀ at the beginning and the end of the colonization experiments were not significant (one factor ANOVA) at the two sites. EC₅₀ was on average 0.89 μM atrazine in the shaded site and 0.29 μM atrazine in the open site. A significant negative correlation between irradiance and EC₅₀ was observed all the experiments were considered together (r = 0.464, n = 20, p<0.05), suggesting that light history may have an important role in the response to atrazine. This investigation reveals that the response of stream periphyton to atrazine is likely to be influenced by colonization time and the corresponding changes in algal density and community composition as well as by environmental conditions (e.g. light regime) throughout succession. This revised version was published online in September 2006 with corrections to the Cover Date.     

In situ localization of PCR-amplified DNA and cDNA

Combining the high sensitivity of PCR with the cell localizing ability ofin situ hybridization allows for the reproducible detection of low copy targets in intact cells. This article describes several key variables that include fixation, protease digestion, the hot start maneuver, stringency, and, for RNA analysis, DNase digestion that are important to successfulin situ PCR. Also stressed is the importance of performing and interpreting controls with each experiment. Important controls include omission of key components, use of samples known either to contain or lack the target of interest and, most importantly, the in-built controls invariably present in the heterogeneous component of any given tissue type.     

Benthic community metabolism in three habitats in an Ozark stream

Benthic community metabolism was measured in three habitats (riffles, runs and pools) during spring (May), summer (July) and fall (October) in the Jacks Fork River, Missouri, using an in situ chamber technique. Net community productivity (NCP) and gross community productivity (GCP) were highest in riffles, lowest in pools and intermediate in runs. Rates of NCP and GCP during spring and fall were similar for both riffles and runs, but NCP and GCP increased significantly during summer in both habitats. Pool substrates were always heterotrophic and exhibited no significant seasonal changes in NCP or GCP. Community respiration (CR) was highest in riffles, intermediate in runs and lowest in pools, but interhabitat differences in CR were generally smaller than for NCP. Rates of CR during spring and fall were similar, but CR increased significantly during summer. Results indicate that the physical conditions associated with each habitat strongly affect benthic community metabolism in this stream and that the relative proportions of these habitats will influence the ratio of living algal:detrital organic matter potentially available for consumers.     

Light,nutrients and the fatty acid composition of stream periphyton

1. While the balance of light and nutrients is known to influence the food quality of herbivores by altering algal phosphorus and nitrogen content, the combined effects of light and nutrients on fatty acid synthesis in freshwater periphyton are relatively unknown. In this study, we manipulated light and phosphorus concentration in large, flow‐through experimental streams to examine their effects on both elemental stoichiometry and fatty acid content in periphyton. 2. Two levels of phosphorus (4 and 80 μg L^?1) and three of light (17, 40, 110 μmol photons m^?2 s^?1) were applied in a factorial design in two separate experiments. Diatoms dominated periphyton communities in both experiments, comprising >95% of algal biovolume. Periphyton growth in the streams was simultaneously affected by both resources, even at low rates of supply. 3. Periphyton C/P and C/N ratios increased with light augmentation and decreased with phosphorus enrichment, and consistent with the light : nutrient hypothesis (LNH). Light effects were strongest in streams with low phosphorus concentrations. 4. Periphyton fatty acids reflected the dominance of diatoms : palmitic (16 : 0), palmitoleic (16 : 1ω7) and eicosapentanoic (20 : 5ω3) were the principal saturated (SAFA), monounsaturated (MUFA) and polyunsaturated fatty acids (PUFA), respectively. Linoleic (18 : 2ω6) and linolenic (18 : 3ω3) acids, characteristic of chlorophytes and cyanophytes, were rare, comprising <2% of total fatty acids. 5. Periphyton fatty acid profiles were highly sensitive to light and phosphorus. The proportion of fatty acids comprised by SAFA and MUFA increased with light augmentation and decreased with phosphorus enrichment, whereas PUFA decreased with light and increased with phosphorus. Light effects on fatty acid composition were strongest in phosphorus‐poor streams. PUFA declined with increasing light/phosphorus ratios in the streams, whereas ‘energy’ fatty acids (16 : 0 and 16 : 1) increased. The ratio of SAFA/PUFA was strongly and positively correlated with C/P and C/N ratios. SAFA and MUFA, normalised to dry mass, increased two‐ to threefold with increasing light, while PUFA normalised to dry mass was not significantly affected by light. 6. Similarities in the responses of fatty acids and elemental stoichiometry to light and phosphorus treatments suggested that they were influenced by a common mechanism. Both components of food quality appeared to be sensitive to light‐regulated rates of carbon fixation which, when coupled with insufficient supplies of phosphorus, caused diatom cells to store surplus carbon in SAFA, MUFA and other carbon‐rich compounds that diluted both essential fatty acids and mineral nutrients.     

Applying the light : nutrient hypothesis to stream periphyton

1. The light : nutrient hypothesis (LNH) states that algal nutrient content is determined by the balance of light and dissolved nutrients available to algae during growth. Light and phosphorus gradients in both laboratory and natural streams were used to examine the relevance of the LNH to stream periphyton. Controlled gradients of light (12–426 μmol photons m^?2 s^?1) and dissolved reactive phosphorus (DRP, 3–344 μg L^?1) were applied experimentally to large flow‐through laboratory streams, and natural variability in canopy cover and discharge from a wastewater treatment facility created gradients of light (0.4–35 mol photons m^?2 day^?1) and DRP (10–1766 μg L^?1) in a natural stream. 2. Periphyton phosphorus content was strongly influenced by the light and DRP gradients, ranging from 1.8 to 10.7 μg mg AFDM^?1 in the laboratory streams and from 2.3 to 36.9 μg mg AFDM^?1 in the natural stream. Phosphorus content decreased with increasing light and increased with increasing water column phosphorus. The simultaneous effects of light and phosphorus were consistent with the LNH that the balance between light and nutrients determines algal nutrient content. 3. In experiments in the laboratory streams, periphyton phosphorus increased hyperbolically with increasing DRP. Uptake then began levelling off around 50 μg L^?1. 4. The relationship between periphyton phosphorus and the light : phosphorus ratio was highly nonlinear in both the laboratory and natural streams, with phosphorus content declining sharply with initial increases in the light : phosphorus ratio, then leveling off at higher values of the ratio. 5. Although light and DRP both affected periphyton phosphorus content, the effects of DRP were much stronger than those of light in both the laboratory and natural streams. DRP explained substantially more of the overall variability in periphyton phosphorus than did light, and light effects were evident only at lower phosphorus concentrations (≤25 μg L^?1) in the laboratory streams. These results suggest that light has a significant negative effect on the food quality of grazers in streams only under a limited set of conditions.     

Seasonality of macrophytes and interaction with flow in a New Zealand lowland stream

Introduced submerged macrophytes have come to dominate many shallow water bodies in New Zealand, and are a common component of many lowland streams. We investigated the seasonal variation of macrophyte abundance, its influence on flow and channel volume, and the implications of this on stream habitat and functioning in Whakapipi Stream, a typical lowland stream draining a predominantly agricultural catchment.Abundance of macrophytes over the summer was primarily controlled by the phenological cycles of the two dominant species. Mean minimum total macrophyte biomass (36 g m^–2) and cover (7%) occurred in winter (June and August, respectively), and mean maximum biomass (324 g m^–2), and cover (79%) occurred in late summer (March and February respectively). Egeria densa comprised the majority of both cover and biomass during the study period, except early summer (December) when Potamogeton crispus was prevalent in the shallow stream reaches.Macrophyte beds had a major impact on summer stream velocities, reducing average velocities by an estimated 41%. Stream cross-sectional area was maintained at relatively stable levels similar to that recorded over winter, when stream discharge was in the order of seven times greater. The mean velocity distribution coefficient (), and Manning's roughness coefficient (n) were dependent on and displayed a positive linear relationship with macrophyte abundance. The velocity distribution coefficient is recommended as a better indicator of macrophyte effects on velocity in natural streams, as it does not assume uniform velocity, channel depth and slope within the stream reach.Our study shows that submerged macrophytes play an important structuring role within the stream during the summer period, where macrophyte beds act as semi-permeable dams, retarding flow velocities and increasing stream depth and cross-sectional area. This promotes habitat heterogeneity by creating a greater range of flow velocity variation, and also provides large stable low-flow areas. Other likely ecosystem effects resulting from macrophyte/velocity interactions include increased sedimentation, potential for nutrient processing and increased primary production, both by macrophytes and attached epiphyton. The complex architecture of submerged macrophytes and their influence on stream flow may also provide an increased diversity of habitat for other aquatic biota. We propose that management of degraded lowland streams such as the Whakapipi Stream to maintain stretches with moderate quantities of submerged macrophytes interspersed with shaded areas would optimise stream health during low summer flows.     

Changes in diversity along a successional gradient in a Costa Rican upper montane Quercus forest

Changes in terrestrial vascular plant diversity along a successional gradient were studied in a Costa Rican upper montane Quercus forest. In 1991 and 1992 species presence and cover were recorded in 12 successional 0.1 ha forest plots. A total of 176 species in 122 genera and 75 families were found. Asteraceae was the most speciose family. With the help of TWINSPAN three successional phases were classified: (i) Early Secondary Forest (ESF, 145 spp.), (ii) Late Secondary Forest (LSF, 130 spp.) and (iii) Primary Forest (PF, 96 spp.). Detrended Correspondence Analysis (DCA) species ordination using DECORANA illustrates that different ecological species groups can be distinguished along the time sequence. Alpha diversity (Shannon-Wiener index, among others) in ESF and LSF was significantly greater than in PF. This is probably explained by downslope migration of numerous sub(alpine) species to cleared and recently abandoned montane sites. Beta diversity applying Sørensen's similarity coefficients declined during succession. Using linear regression, the minimum time required for floristic recovery following disturbance and abandonment was calculated at 65.9 years. A comparison with other studies shows that secondary forests in upper montane Costa Rica can be as diverse as in neotropical lowlands.     

High nutrient availability leads to weaker top‐down control of stream periphyton: Compensatory feeding in Ancylus fluviatilis

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In situ observation of suspended solid aggregates in rivers

Suspended solids are a major pathway of the biogeochemical fate of many contaminants in aquatic systems. Aggregation processes of particles are poorly reported in rivers but they are likely to exist at low flow, mostly because of sticky polysaccharides produced by living organisms. These processes affect suspended particle transport by changing particle sizes and densities and may also limit exchanges of matter between solid and dissolved phases. The main difficulty in floc studies is aggregate fragility, which requires the use of specialized in situ techniques to analyze aggregated suspended solids.We describe two in situ methods for observing suspended particles which do not need heavy field equipment. The first one is based on the filtration of a thin water layer in the natural flow through a membrane which can subsequently be observed by microscope. The second one is based on in situ video snapshots of suspended solids by an endoscope. The video camera linked to the microscope or the endoscope supplies images which are automatically analyzed by image processing to give size distributions.Procedures and validation for both methods are described and results compared with a standard method. The filtration method has been used to trace suspended solids from sewer overflows in the Seine River downstream of Paris. Freshwater flocs are described and a discussion of the fate of aggregates is presented.

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Résumé Les matières en suspension sont déterminantes dans le cycle biogéochimique de nombreux polluants des systèmes aquatiques. Les phénomènes d'agrégation des particules sont encore mal connus en rivière, mais peuvent se produire dans les fleuves urbains du fait de la lenteur des écoulements et vraisemblablement de l'importance des processus bactériens. Ces phénomènes influencent directement le transport des suspensions en modifiant les tailles et les densités des particules. Ils peuvent également limiter les échanges chimiques entre phase dissoute et particulaire.Le problème de la fragilité des flocs et la complexité des équipements habituellement utilisés in situ nous ont conduit à développer deux méthodes d'observation non destructives des flocs. La première consiste à filtrer une mince lame d'eau directement dans l'écoulement naturel puis à observer les suspensions au microscope. La deuxième méthode est l'observation directe des suspensions dans l'écoulement, grâce à un endoscope. Une caméra vidéo reliée au microscope ou à l'endoscope fournit des images que l'on traite automatiquement (dénombrement et mesure des particules) pour obtenir la granulométrie des agrégats naturels.Nous comparons les résultats des deux méthodes à ceux d'une méthode de référence, puis nous comparons les deux méthodes entre elles. La filtration in situ a été utilisée en Seine à l'aval de gros rejets de temps de pluie de l'agglomération parisienne pour étudier les matières en suspension issues des rejets. La caractérisation des flocs de Seine permet de discuter de leur devenir dans le fleuve.

     

人单拷贝及重复DNA序列的原位PCR

在培养的人小肠癌转移腹水细胞系细胞中进行了Y染色体特异的重复序列及单拷贝序列的原位扩增与检测.结果显示原位PCR法的灵敏度比直接的原位杂交法明显提高.     

Resin-core and buried-bag estimates of nitrogen transformations in Costa Rican lowland rainforests

We compared the resin-core and buried-bag incubation methods for estimating nitrogen (N) transformation rates using the ¹⁵N pool dilution technique in alluvial soils of an early successional forest (ESF) and an old-growth forest (OGF) at the La Selva Biological Station in Costa Rica. Soil cores (38×100-mm) from both forests were incubated in situ for 7 days. The two methods gave generally similar estimates of net N mineralization rates for the two forests. Estimates of ammonium production by the resin-core method were higher than those by the buried-bag method in ESF, but did not differ significantly in OGF (p<0.05). Estimates of nitrate production by the two methods did not differ significantly. Nitrate averaged 74% and 81% of the total inorganic N production in ESF and OGF, respectively. Net N mineralization in ESF (6.6 mmol m^-2d^-1) did not differ significantly from that in OGF (5.0 mmol m^-2d^-1). Fluxes of ammonium and nitrate were high for both forests, but the OGF tended to have higher gross mineralization and nitrification rates than ESF. Approximately 60% of the gross nitrate production and less than 30% of the ammonium were immobilized by microorganisms.     

Application of universally amplifying plastid primers to environmental sampling of a stream periphyton community

To demonstrate the utility of universal plastid primers for probing of environmental samples, we extracted DNA from a tropical stream periphyton community and created two environmental clone libraries. We demonstrate the recovery of DNA sequences corresponding to the major groups of algae observed microscopically in the sample, illustrating the utility of these primers for analysis of environmental samples. Using a touchdown polymerase chain reaction technique, almost 99% of recovered sequences correspond to plastid-containing or cyanobacterial taxa, which allows algae to be targeted to the almost complete exclusion of noncyanobacterial prokaryotes and nonplastid-containing eukaryotes.     

In situ study of chorion gene amplification in ovarian follicle cells ofDrosophila nasuta

The temporal and spatial pattern of replication of chorion gene clusters in follicle cells during oogenesis inDrosophila melanogaster andDrosophila nasuta was examined by [^3H thymidine autoradiography and byin situ hybridization with chorion gene probes. When pulse labelled with [³H] thymidine, the follicle cells from stage 10–12 ovarian follicles of bothDrosophila melanogaster and,Drosophila nasuta often showed intense labelling at only one or two sites per nucleus.In situ hybridization of chorion gene probes derived fromDrosophila melanogaster with follicle cell nuclei ofDrosophila melanogaster andDrosophila nasuta revealed these discrete [³H] thymidine labelled sites to correspond to the two amplifying chorion gene clusters. It appears, therefore, that in spite of evolutionary divergence, the organization and programme of selective amplification of chorion genes in ovarian follicle cells have remained generally similar in these two species. The endoreplicated and amplified copies of each chorion gene cluster remain closely associated but the two clusters occupy separate sites in follicle cell nucleus.     

In situ predatory behavior ofMysis relicta in Lake Michigan

Selectivity coefficients (W) and predation rates on Lake Michigan zooplankton were determined forMysis relicta during spring through fall using anin situ method. W values indicated the following ranked order of prey preference: Cladocera > copepod copepodites and copepod nauplii > adult diaptomids and cyclopoids. With few exceptions, W values for different prey categories remained fairly constant despite greatly changing relative abundances of prey. Predation rates and prey selectivity were similar in most cases to those determined in laboratory studies. Ingestion rates (percent dry body weight · day^–1) were correlated to total prey biomass (r = 0.38) and to effective prey biomass (r = 0.85), where the weighting factors were overall mean selectivity coefficients for the different prey categories. This result suggested that seasonally varying composition of prey caused much of the variation in ingestion rates among experiments. Feeding trials performed at the same depth with daytime and nighttime assemblages of zooplankton indicated that Cladocera may escape heavyMysis predation at night by migrating from the metalimnetic-hypolimnetic interface into the epilimnion.Contribution 333 from the Great Lakes Research Division, The University of Michigan and contribution 287 from the Great Lakes Environmental Research Laboratory, National Oceanic and Atmospheric Administration.Contribution 333 from the Great Lakes Research Division, The University of Michigan and contribution 287 from the Great Lakes Environmental Research Laboratory, National Oceanic and Atmospheric Administration.     

In situ clearance rates of planktonic rotifers

The in situ clearance rates of several rotifer species from a small, temperate eutrophic lake were measured using three radioactive tracer cell-types, a bacterium (Aerobacter), a yeast (Rhodoto-rula), and alga (Chlamydomonas). Rates were below 10 µl/anim/h but varied significantly among species. Keratella cochlearis, Kellicottia bostoniensis, and Conochilus dossuarius ingested all three tracer cells but rates varied substantially with tracer cell-type. Polyarthra dolichoptera and P. euryptera ingested only the algal cells. Co-occurring forms of K. cochlearis and species of Polyarthra differed markedly in size and in tracer cell utilization, indicating niche diversification in food resources.