Total phosphorus inference models and indices for coastal plain streams based on benthic diatom assemblages from artificial substrates

We investigated the potential for using diatoms to monitor and assess nutrient enrichment in coastal plain streams using weighted-averaging inference models and diatom trophic indices. Samples were collected from low-gradient, clay- to sand-bottom streams in New Jersey (NJ), USA, using artificial substrates (diatometers). Multivariate analysis showed that conductivity was overall the most important explanatory variable. Total phosphorus (TP) explained a significant proportion of the variation in diatom species composition. There was statistical justification for development of inference models for TP but not for total nitrogen (TN). We developed and tested models for inferring TP using weighted-averaging (WA) and weighted-averaging partial least squares (WA-PLS) regression and calibration techniques. We also created a diatom TP index by rescaling the inferred TP values. WA-PLS provided the best model (n = 38), which showed moderate predictive ability (r _boot² = 0.43; RMSEP_boot = 0.30 log₁₀ μg l⁻¹ TP); it performed best at lower TP concentrations and tended to underestimate values above 100 μg l⁻¹. The TP index performed well; it assigned the majority of the index scores to the correct nutrient category. TP models and indices developed for the Coastal Plain had lower predictive ability than those developed for northern NJ and streams in other comparable geographic regions of the US. This lower performance can be attributed primarily to a data gap in the TP gradient in the calibration dataset (lack of sites with TP concentrations between 240 and 560 μg l⁻¹), and a smaller number of samples. We conclude that diatom-based TP inference models and artificial substrate sampling are useful for assessing and monitoring nutrient enrichment in coastal plain streams. Given the worldwide distribution of streams similar to those in this study, these tools should be widely applicable. Handling editor: D. Ryder     

A comparison of algal,macroinvertebrate, and fish assemblage indices for assessing low-level nutrient enrichment in wadeable Ozark streams

Biotic indices for algae, macroinvertebrates, and fish assemblages can be effective for monitoring stream enrichment, but little is known regarding the value of the three assemblages for detecting perturbance as a consequence of low-level nutrient enrichment. In the summer of 2006, we collected nutrient and biotic samples from 30 wadeable Ozark streams that spanned a nutrient-concentration gradient from reference to moderately enriched conditions. Seventy-three algal metrics, 62 macroinvertebrate metrics, and 60 fish metrics were evaluated for each of the three biotic indices. After a group of candidate metrics had been identified with multivariate analysis, correlation procedures and scatter plots were used to identify the four metrics having strongest relations to a nutrient index calculated from log transformed and normalized total nitrogen and total phosphorus concentrations. The four metrics selected for each of the three biotic indices were: algae—the relative abundance of most tolerant diatoms, the combined relative abundance of three species of Cymbella, mesosaprobic algae percent taxa richness, and the relative abundance of diatoms that are obligate nitrogen heterotrophs; macroinvertebrate—the relative abundance of intolerant organisms, Baetidae relative abundance, moderately tolerant taxa richness, and insect biomass; fish—herbivore and detritivore taxa richness, pool species relative abundance, fish catch per unit effort, and black bass (Micropterus spp.) relative abundance.All three biotic indices were negatively correlated to nutrient concentrations but the algal index had a higher correlation (rho = ?0.89) than did the macroinvertebrate and fish indices (rho = ?0.63 and ?0.58, respectively). Biotic index scores were lowest and nutrient concentrations were highest for streams with basins having the highest poultry and cattle production. Because of the availability of litter for fertilizer and associated increases in grass and hay production, cattle feeding capacity increases with poultry production. Studies are needed that address the synergistic effect of poultry and cattle production on Ozark streams in high production areas before ecological risks can be adequately addressed.     

Impact of nutrient enrichment and alkalinization on periphyton communities in the New Jersey Pine Barrens

The impact of residential and agricultural development on stream periphyton communities in the New Jersey Pine Barrens was examined by comparison with communities in undeveloped areas. Watershed disturbance resulted in stream water primarily characterized by greatly elevated pH levels and nitrate concentrations. A total of 53 periphyton species were encountered in bimonthly samples over a one year period in the three disturbed and three undisturbed study streams. Species richness was significantly greater in the disturbed streams based on three criteria: the average number of species per stream on each sampling occasion (disturbed = 6.3; undisturbed = 4.9), the average number of species per stream for the entire year (disturbed = 19.3; undisturbed = 16.0), and the total number of species found in streams within a type (disturbed = 40; undisturbed = 31). Species composition also changed significantly as the result of disturbance. There appeared to be replacement of species characteristic of undisturbed Pine Barrens streams with species peripheral to the region. The expected effects of both elevated pH and nitrate were consistent with these results.     

Effects of nutrient enrichment on boreal streams: invertebrates, fungi and leaf-litter breakdown

1. The effect of nutrient enrichment on structural (invertebrate indices) and functional (leaf‐litter breakdown rates) characteristics of stream integrity was studied in nine boreal streams. 2. The results showed predicted changes in biotic indices and leaf‐litter breakdown along a complex (principal component) nutrient gradient. Biotic indices were better correlated with nutrient effects than leaf‐litter breakdown. 3. Fungal biomass and invertebrate densities in the litter bags were positively correlated with leaf‐litter breakdown, and both were also positively related to the nutrient gradient. 4. Invertebrate community composition influenced breakdown rate. High breakdown rates at one site were associated with the high abundance of the detritivore Asellus aquaticus. 5. This study lends support to the importance of invertebrate and fungi as mediators of leaf‐litter decomposition. However, our study also shows that study design (length of incubation) can confound the interpretation of nutrient‐induced effects on decomposition.     

Relationships between nutrient enrichment,pleurocerid snail density and trematode infection rate in streams

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Effects of nutrient enrichment on the decomposition of wood and associated microbial activity in streams

1. We determined the effects of nutrient enrichment on wood decomposition rates and microbial activity during a 3‐year study in two headwater streams at Coweeta Hydrologic Laboratory, NC, U.S.A. After a 1‐year pretreatment period, one of the streams was continuously enriched with inorganic nutrients (nitrogen and phosphorus) for 2 years while the other stream served as a reference. We determined the effects of enrichment on both wood veneers and sticks, which have similar carbon quality but differ in physical characteristics (e.g. surface area to volume ratios, presence of bark) that potentially affect microbial colonisation and activity. 2. Oak wood veneers (0.5 mm thick) were placed in streams monthly and allowed to decompose for approximately 90 days. Nutrient addition stimulated ash‐free dry mass loss and increased mean nitrogen content, fungal biomass and microbial respiration on veneers in the treatment stream compared with the reference. The magnitude of the response to enrichment was great, with mass loss 6.1 times, and per cent N, fungal biomass and microbial respiration approximately four times greater in the treatment versus reference stream. 3. Decomposition rate and nitrogen content of maple sticks (ca. 1–2 cm diameter) also increased; however, the effect was less pronounced than for veneers. Wood response overall was greater than that determined for leaves in a comparable study, supporting the hypothesis that response to enrichment may be greater for lower quality organic matter (high C : N) than for higher quality (low C : N) substrates. 4. Our results show that moderate nutrient enrichment can profoundly affect decomposition rate and microbial activity on wood in streams. Thus, the timing and availability of wood that provides retention, structure, attachment sites and food in stream ecosystems may be affected by nutrient concentrations raised by human activities.     

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.     

Root allocation and multiple nutrient limitation in the New Jersey Pinelands

Abstract Current understanding of the effects of resource stress on plant communities emphasizes the adaptive integration of multiple limiting factors, but it has been difficult to directly demonstrate the fundamental assumption of the adaptive control of limitation. One model predicts a positive correlation between optimal allocation to the uptake of each resource and growth response to enrichment of that resource. Here we report a test of this prediction by a fertilization experiment in the New Jersey Pinelands Biosphere Reserve where limitation was measured by growth response to nutrient enrichments, and allocation was measured by root proliferation in microsites enriched by those same nutrients. Results suggest that a stand of regenerating Pinus echinata Mill. (shortleaf pine) was jointly limited by nitrogen and potassium, with a possible small effect of phosphorus. Root allocation was proportional to growth response, which supports the assumption of adaptive control of limitation.     

Relationships between benthic biota and hydrological indices in New Zealand streams

1. The objective of this study was to identify the most ecologically relevant hydrological indices for characterizing hydrological regimes in New Zealand streams. To do this we related measures of periphyton chlorophyll a, ash-free dry mass (AFDM), species richness, and diversity and invertebrate density, species richness and diversity, to thirty-four hydrological variables derived from daily flow records at eighty-three sites. The hydrological variables included some describing average flow conditions, flow variability, floods, and low-flow characteristics. 2. A principal components analysis showed that the interrelationship between many of the hydrological variables was high, and most variables correlated significantly with Principal Component 1 (PC1). The flood frequency variables formed a distinct component of the flow regime and were the main contributor to PC2. 3. We found that both the average flow conditions and some measure of variability were significantly related to most of the biological variables, and these individual hydrological variables were more strongly correlated to the biological measures than the composite principal components. Only four of the thirty-four flow variables were significantly correlated (P < 0.05) with measures of periphyton biomass (chlorophyll a and AFDM), whereas twenty-four variables were correlated with periphyton diversity. Conversely, thirty-one of the thirty-four flow variables were correlated with total invertebrate density, whereas only four variables correlated with diversity. 4. We selected the flood frequency (FRE₃), where a flood is defined as flows higher than three times the median flow, as the most ecological useful overall flow variable in New Zealand streams because it explained a significant amount of the variance in four out of the six main benthic community measures, and it had a clear mechanism of control of the biota which was commensurate with current stream ecosystem theory. Periphyton biomass decreased with increasing FRE₃, whereas invertebrate density had an increasing/curvilinear relationship with FRE₃. Periphyton species richness and diversity decreased with increasing FRE₃.     

A meta‐analysis of the effects of nutrient enrichment on litter decomposition in streams

The trophic state of many streams is likely to deteriorate in the future due to the continuing increase in human‐induced nutrient availability. Therefore, it is of fundamental importance to understand how nutrient enrichment affects plant litter decomposition, a key ecosystem‐level process in forest streams. Here, we present a meta‐analysis of 99 studies published between 1970 and 2012 that reported the effects of nutrient enrichment on litter decomposition in running waters. When considering the entire database, which consisted of 840 case studies, nutrient enrichment stimulated litter decomposition rate by approximately 50%. The stimulation was higher when the background nutrient concentrations were low and the magnitude of the nutrient enrichment was high, suggesting that oligotrophic streams are most vulnerable to nutrient enrichment. The magnitude of the nutrient‐enrichment effect on litter decomposition was higher in the laboratory than in the field experiments, suggesting that laboratory experiments overestimate the effect and their results should be interpreted with caution. Among field experiments, effects of nutrient enrichment were smaller in the correlative than in the manipulative experiments since in the former the effects of nutrient enrichment on litter decomposition were likely confounded by other environmental factors, e.g. pollutants other than nutrients commonly found in streams impacted by human activity. However, primary studies addressing the effect of multiple stressors on litter decomposition are still few and thus it was not possible to consider the interaction between factors in this review. In field manipulative experiments, the effect of nutrient enrichment on litter decomposition depended on the scale at which the nutrients were added: stream reach > streamside channel > litter bag. This may have resulted from a more uniform and continuous exposure of microbes and detritivores to nutrient enrichment at the stream‐reach scale. By contrast, nutrient enrichment at the litter‐bag scale, often by using diffusing substrates, does not provide uniform controllable nutrient release at either temporal or spatial scales, suggesting that this approach should be abandoned. In field manipulative experiments, the addition of both nitrogen (N) and phosphorus (P) resulted in stronger stimulation of litter decomposition than the addition of N or P alone, suggesting that there might be nutrient co‐limitation of decomposition in streams. The magnitude of the nutrient‐enrichment effect on litter decomposition was higher for wood than for leaves, and for low‐quality than for high‐quality leaves. The effect of nutrient enrichment on litter decomposition may also depend on climate. The tendency for larger effect size in colder regions suggests that patterns of biogeography of invertebrate decomposers may be modulating the effect of nutrient enrichment on litter decomposition. Although studies in temperate environments were overrepresented in our database, our meta‐analysis suggests that the effect of nutrient enrichment might be strongest in cold oligotrophic streams that depend on low‐quality plant litter inputs.     

Experimental nutrient enrichment of forest streams increases energy flow to predators along greener food‐web pathways

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Effects of nutrient enrichment on C and N stable isotope ratios of invertebrates,fish and their food resources in boreal streams

Carbon and nitrogen stable isotopes are frequently used to study energy sources and food web structure in ecosystems, and more recently, to study the effects of anthropogenic stress on aquatic ecosystems. We investigated the effect of nutrient enrichment on δ¹³C and δ¹⁵N in fine (FPOM), coarse (CPOM) particulate organic matter, periphyton, invertebrates and fish in nine boreal streams in south-central Sweden. In addition, we analysed the diet of benthic consumers using stable isotope data. Increases in δ¹⁵N of periphyton (R ² = 0.88), CPOM (0.78), invertebrates (0.92) and fish (0.89) were related to nutrient enrichment. In contrast, δ¹³C signatures did not change along the nutrient gradient. Our results show that δ¹⁵N has potential as a sensitive indicator of nutrient enrichment in boreal streams. Carbon and nitrogen isotopes failed to elucidate putative diets of selected aquatic consumers. Indeed, comparison of low- and high-impact sites showed that δ¹³C of many consumers were found outside the ranges of basal resource δ¹³C. Moreover, ranges of basal resource δ¹³C and δ¹⁵N overlapped at both low and high sites, making discrimination between the importance of allochthonous and autochthonous production difficult. Our findings show that a fractionation rate of 3.4‰ is not always be appropriate to assess trophic interactions, suggesting that more studies are needed on fractionation rates along gradients of impairment. Handling editor: M. Power     

Regional nutrient thresholds in wadeable streams of New York State protective of aquatic life

Human influence on the landscape has caused nutrients in surface waters to increase to the point where their presence has substantially altered biological communities. Because this is a nationally recognized problem, the United States Environmental Protection Agency (USEPA) tasked each state, tribe, and territory to adopt numeric nutrient criteria. Here we integrate the concept of ecological thresholds with the derivation of effects-based numeric nutrient criteria. Acceptable levels of risk exceeding predefined biocriteria were determined using conditional probability and nonparametric changepoint analysis. We show how certain community metrics exhibit threshold responses to nutrients. Using these thresholds, we suggest nutrient values protective of aquatic life and characterize community composition. Nutrient criteria were suggested for two aggregations of USEPA's nutrient ecoregions in New York State an upland pristine forested region (Ecoregions VIII and XI) and a nutrient-enriched lowland region (Ecoregions VII and XIV). Of 11 biological community metrics evaluated, 5 had a strong response to nutrients (NBI-P, NBI-N, HBI, TRI, and DMA). Maximum probabilities of exceeding the biological impairment thresholds established for these metrics ranged from 81% to 100%. Changepoint analysis conducted on probability outcomes of these metrics resulted in nutrient thresholds at or above USEPA nutrient guidance values, depending on ecoregion and nutrient variable (Ecoregion VIII/XI: 15 μg/L TP, 472 μg/L TN, 150 μg/L NO₃-N, Ecoregion VII/XIV: 17 μg/L TP, 1133 μg/L TN, 356 μg/L NO₃-N). Results of taxonomic similarity percentages (SIMPER) and species contributions indicate that several orders of macroinvertebrates and diatoms exhibit significant shifts in their percent of contributions to sample similarity in response to changes in nutrient concentrations.     

The use of periphyton communities for nutrient removal from polluted streams

The results of experiments on the efficiency of periphyton communities for nutrient removal from polluted streams in a continuous flow-through are given. The artifical stream (5 m × 0.7 m × 0.5 m) was made of wood, with silon (a kind of nylon) screens, as a substratum for periphyton growth. The elimination of nutrients was monitored by ammonium, nitrite, nitrate and orthophosphate analyses. In addition, the elimination of organics and the decrease in trophic state were determined. During two field experiments a marked elimination of nitrogen and phosphorus was demonstrated. The maximum efficiency of ammonium and orthophosphate removal was 80% and 70%, respectively. Organic removal reached 35% (C.O.D._Mn-Kubel) and 54% (B.O.D.₅). Inorganic and organic nutrient elimination caused significant changes in periphyton community structure in the outflow portion of the through, evaluated by the saprobic index and the similarity coefficient. The experiments confirmed that periphyton communities are a useful means of nutrient removal from polluted streams.     

Recursive computing and simulation-free inference for general factorizable models

We illustrate how the recursive algorithm of Reeves & Pettitt(2004) for general factorizable models can be extended to allowexact sampling, maximization of distributions and computationof marginal distributions. All of the methods we describe applyto discrete-valued Markov random fields with nearest neighbourintegrations defined on regular lattices; in particular we illustratethat exact inference can be performed for hidden autologisticmodels defined on moderately sized lattices. In this contextwe offer an extension of this methodology which allows approximateinference to be carried out for larger lattices without resortingto simulation techniques such as Markov chain Monte Carlo. Inparticular our work offers the basis for an automatic inferencemachine for such models.     

Automated refinement and inference of analytical models for metabolic networks

The reverse engineering of metabolic networks from experimental data is traditionally a labor-intensive task requiring a priori systems knowledge. Using a proven model as a test system, we demonstrate an automated method to simplify this process by modifying an existing or related model--suggesting nonlinear terms and structural modifications--or even constructing a new model that agrees with the system's time series observations. In certain cases, this method can identify the full dynamical model from scratch without prior knowledge or structural assumptions. The algorithm selects between multiple candidate models by designing experiments to make their predictions disagree. We performed computational experiments to analyze a nonlinear seven-dimensional model of yeast glycolytic oscillations. This approach corrected mistakes reliably in both approximated and overspecified models. The method performed well to high levels of noise for most states, could identify the correct model de novo, and make better predictions than ordinary parametric regression and neural network models. We identified an invariant quantity in the model, which accurately derived kinetics and the numerical sensitivity coefficients of the system. Finally, we compared the system to dynamic flux estimation and discussed the scaling and application of this methodology to automated experiment design and control in biological systems in real time.     

Alteration of phytoplankton phosphorus status during enrichment experiments: implications for interpreting nutrient enrichment bioassay results

We compared the results of phosphorus-enrichment bioassay experiments with alkaline phosphatase activity (APA) assays as indicators of phosphorus (P) limitation of in situ phytoplankton growth. In 4-d experiments, phytoplankton APA decreased or remained unchanged in P-enriched samples, but increased in unenriched samples, indicating a rapid alteration of the P status of the unenriched algae during the experimental incubations. In direct comparisons of enrichment bioassays and APA assays of reservoir phytoplankton samples, the results of the two methods corresponded in general, although contradictory results were not uncommon. Our data support the conclusion that enrichment experiments can indicate the potential for nutrient limitation of algal growth in the absence of other limiting factors, but do not necessarily demonstrate the occurrence of in situ nutrient limitation of phytoplankton production.     

Likelihood-based inference for stochastic models of sexual network formation

Sexually-transmitted diseases (STDs) constitute a major public health concern. Mathematical models for the transmission dynamics of STDs indicate that heterogeneity in sexual activity level allow them to persist even when the typical behavior of the population would not support endemicity. This insight focuses attention on the distribution of sexual activity level in a population. In this paper, we develop several stochastic process models for the formation of sexual partnership networks. Using likelihood-based model selection procedures, we assess the fit of the different models to three large distributions of sexual partner counts: (1) Rakai, Uganda, (2) Sweden, and (3) the USA. Five of the six single-sex networks were fit best by the negative binomial model. The American women's network was best fit by a power-law model, the Yule. For most networks, several competing models fit approximately equally well. These results suggest three conclusions: (1) no single unitary process clearly underlies the formation of these sexual networks, (2) behavioral heterogeneity plays an essential role in network structure, (3) substantial model uncertainty exists for sexual network degree distributions. Behavioral research focused on the mechanisms of partnership formation will play an essential role in specifying the best model for empirical degree distributions. We discuss the limitations of inferences from such data, and the utility of degree-based epidemiological models more generally.     

Scalable and flexible inference framework for stochastic dynamic single-cell models

Understanding the inherited nature of how biological processes dynamically change over time and exhibit intra- and inter-individual variability, due to the different responses to environmental stimuli and when interacting with other processes, has been a major focus of systems biology. The rise of single-cell fluorescent microscopy has enabled the study of those phenomena. The analysis of single-cell data with mechanistic models offers an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. However, extracting mechanistic information from single-cell data has proven difficult. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic (e.g. variations in chemical reactions) and extrinsic (e.g. variability in protein concentrations) noise. Although several inference methods exist, the availability of efficient, general and accessible methods that facilitate modelling of single-cell data, remains lacking. Here we present a scalable and flexible framework for Bayesian inference in state-space mixed-effects single-cell models with stochastic dynamic. Our approach infers model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. We demonstrate the relevance of our approach by studying how cell-to-cell variation in carbon source utilisation affects heterogeneity in the budding yeast Saccharomyces cerevisiae SNF1 nutrient sensing pathway. We identify hexokinase activity as a source of extrinsic noise and deduce that sugar availability dictates cell-to-cell variability.