Phytoplankton community metrics based on absolute and relative abundance and biomass: implications for multivariate analyses

Phytoplankton and water samples were collected at 12 locations along the temperate lowland Rideau River, Ontario, Canada. The stations were visited twice a month from May to September 1998, 1999, and 2000. Phytoplankton communities were quantified based on cell abundance, entity abundance (colonies, filaments or free-living cells) and biomass (converted from biovolume estimates based on cell shape and biometry), and were expressed as absolute and relative values. The resulting phytoplankton dataset was composed of six different metrics. The general objective was to assess which metric best explained the spatial and temporal variability in the phytoplankton communities of the Rideau River in response to fluctuating environmental variables. Relationships between phytoplankton metrics and water quality variables were assessed using canonical correspondence analyses. The absolute cell abundance metric showed the best relationship with water quality, followed by the cell entity metric. The biomass metric showed the poorest relationship with water quality variables, indicating that accounting for cell size does not provide additional information. The data expressed as absolute values were consistently better predictors of water quality compared to relative values.     

Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data

Mass spectrometry (MS)-based shotgun proteomics allows protein identifications even in complex biological samples. Protein abundances can then be estimated from the counts of tandem MS (MS/MS) spectra attributable to each protein, provided one accounts for differential MS detectability of contributing peptides. We developed a method, APEX, which calculates Absolute Protein EXpression levels based upon learned correction factors, MS/MS spectral counts and each protein's probability of correct identification. This protocol describes APEX-based calculations in three parts. (i) Using training data, peptide sequences and their sequence properties, a model is built to estimate MS detectability (O(i)) for any given protein. (ii) Absolute protein abundances are calculated from spectral counts, identification probabilities and the learned O(i)-values. (iii) Simple statistics allow calculation of differential expression in two distinct biological samples, i.e., measuring relative protein abundances. APEX-based protein abundances span 3-4 orders of magnitude and are applicable to mixtures of 100s to 1,000s of proteins.     

Comparison of three vegetation monitoring methods: Their relative utility for ecological assessment and monitoring

Vegetation cover and composition are two indicators commonly used to monitor terrestrial ecosystems. These indicators are currently quantified with a number of different methods. The interchangeability and relative benefits of different methods have been widely discussed in the literature, but there are few published comparisons that address multiple criteria across a broad range of grass- and shrub-dominated communities, while keeping sampling effort (time) approximately constant. This study compared the utility of three field sampling methods for ecological assessment and monitoring: line-point intercept, grid-point intercept, and ocular estimates. The criteria used include: (1) interchangeability of data, (2) precision, (3) cost, and (4) value of each method based on its potential to generate multiple indicators. Foliar cover by species was measured for each method in five plant communities in the Chihuahuan Desert. Line- and grid-point intercept provide similar estimates of species richness which were lower than those based on ocular estimates. There were no differences in the precision of the number of species detected. Estimates of foliar cover with line- and grid-point intercept were similar and significantly higher than those based on ocular estimates. Precision of cover estimates with line-point intercept was higher than for ocular estimates. Time requirements for the three methods were similar, despite the fact that the point-based methods included cover estimates for all canopy layers and the soil surface, while the ocular estimates included only the top canopy layer. Results suggest that point-based methods provide interchangeable data with higher precision than ocular estimates. Moreover these methods can be used to generate a much greater number of indicators that are more directly applicable to a variety of monitoring objectives, including soil erosion and wildlife habitat.     

Comparison of denitrification characteristics among three habitat types of a large river floodplain: Atchafalaya River Basin,Louisiana

Mobile forms of nitrogen leach from upland environments into aquatic systems, often discharging to coastal zones. Addition of nitrogen to once N-limited systems results in a host of changes ranging from eutrophication to loss of biodiversity. Floodplains can ameliorate these changes by removing and sequestering nitrogen. In many coastal floodplains, sedimentation causes lakes to transition to baldcypress swamps, and ultimately to bottomland hardwood (BLHW) forests. These habitats differ in their contact with floodwater, which directly and indirectly affects their ability to process nutrients, but the effects of habitat change on denitrification at the floodplain scale cannot be predicted because of lack of suitable data. This study compared denitrification characteristics among the aforementioned habitats within the Atchafalaya River Basin (ARB). Microcosms were established in the laboratory, and the acetylene block technique was used to estimate four denitrification characteristics: background denitrification rates, maximum rates, time to reach maximum rates, and the linear response of denitrification to nitrate concentration. There were significant differences in denitrification characteristics among the three habitat types; specifically, all habitats differed in the time required for denitrification to respond to nitrate in the overlying water, and denitrification in lake habitats differed from both BLHWs and baldcypress swamps. Landscape-scale models should account for different linear relationships between denitrification and nitrate concentrations, and different response times to nitrate concentrations for different habitats. Because denitrification characteristics differ across habitats within the ARB, continued habitat change within the floodplain will alter nutrient discharge to coastal waters.     

Assessing noninvasive hair and fecal sampling for monitoring the distribution and abundance of river otter

Monitoring the distribution and abundance of populations is an important component of efforts to meet management or conservation goals. Although the objectives for such studies are easy to define, cost-effective, precise, and accurate estimates are often elusive. We tested the efficacy and compared the cost-effectiveness of methods for estimating the number and recording the distribution of river otter (Lontra canadensis). We genotyped otter hair sampled using two noninvasive instruments and compared those results with a hypothetical study design based on DNA extracted from fecal matter. Patterns of distribution generated from DNA collected at latrine sites were then compared to observations of otter collected using VHF radiotelemetry. We achieved a high probability of genotyping river otter with a small number of hairs (i.e., 59.0 % probability of producing a genotype with 1 guard hair and >5 under hair samples) collected using wire body snares and knaplock hair snags. Body snares were more effective at collecting otter hair, but there was relatively little additional cost to using both sampling instruments. Genotyped hair resulted in a high multi-year recapture rate (61.9 %). Hair collection and genotyping was the most cost-effective method for monitoring populations of river otter ($168.50 US/datum) followed by radiotelemetry ($264.50 US/datum), and the extraction of DNA from fecal matter ($266.00 US/datum). However, the noninvasive techniques did not represent the full distribution and fine-scale movements of otter, as observed using radiotelemetry. There has been much recent reporting of the efficacy of fecal matter as a source of DNA for conducting mark–recapture population estimates for mesocarnivores. Our data suggested that collecting DNA in hair may be a more cost-effective and efficient approach.     

Feeding ecology and ecomorphology of cichlid assemblages in a large Mesoamerican river delta

Fish assemblages in tropical lowland rivers are characterized by a high richness of species that feed on a diverse array of food resources. Although closely related species often have similar feeding ecology, species within the family Cichlidae display a broad spectrum of trophic niches, and resource partitioning has been inferred from studies conducted in Neotropical rivers. We investigated interspecific variation in food resource use and its relationship to morphological variation among cichlid fishes within the Pantanos de Centla Biosphere Reserve, a coastal area encompassing the delta of the Grijalva-Usumacinta River in Tabasco, Mexico. Most species consumed benthic crustaceans, aquatic insect larvae, and detritus, but some were more herbivorous, and one species was a specialized piscivore. Dietary niche overlap among species was higher than expected for one assemblage, and similar to random expectations for another, suggesting a lesser role for resource partitioning than has been shown for some cichlid assemblages, perhaps due to availability of abundant resources, even in low-water conditions. Canonical correspondence analysis revealed that greatest morphological differences am7ong species involved functional traits directly associated with resource use. Relationships between feeding ecology and morphology were similar to those described for other riverine cichlids. Strong ecomorphological relationships facilitate inferences about the ecology of cichlid species, including species that currently lack data from field studies. Knowledge of ecological relationships will be important for conservation in the Pantanos de Centla, an ecosystem of global significance for biodiversity and ecosystem services.     

A comparison of fixatives for the estimation of abundance and biovolume of marine planktonic ciliate populations

The effects of five treatments with four commonly used fixativeson the abundance and cell volume of marine planktonic ciliateswere investigated on a natural community from Plymouth Sound.The fixative treatments were 5% and 9% Bouin's solution, 0.4%acid Lugol's iodine, 1% buffered formaldehyde and 1% glutaraldehyde.The abundance of the aloricate ciliate community varied accordingto fixative treatment, with Lugol's maintaining the greatestcell numbers, followed by Bouin's, glutaraldehyde and formaldehyde.The effects of the fixatives on the abundance of the two mostcommon aloricate taxa, Balanion sp. and Strombidium epidemumwere similar to, and components of, those for the aloricatepopulation as a whole. However, there was little differencebetween the effects of different fixatives on the abundanceof the tintinnid community, or on the abundance of the mostcommon tintinnid, Tintinnopsis nana. Mean cell volumes of Balanionsp., S.epidemum and T.nana were greatest in samples fixed informaldehyde, followed by glutaraldehyde, Lugol's and Bouin's.The mean population volume of the aloricate and tintinnid populationsgenerally reflected this trend with greatest values recordedin formaldehyde- and glutaraldehyde-fixed samples, followedby Lugol's and Bouin's; however, the differential effects ofthe fixatives were not as great. Lugol's therefore appears tobe the most effective fixative tested for the estimation ofciliate abundance and population volume, the latter being afunction of abundance and cell volume. ³Present address: British Antarctic Survey, High Cross, MadingleyRoad, Cambridge CB3 OET, UK     

Species temporal variability: epigaeic ant assemblages and management for abundance and scarcity

Summary Ant assemblages in five closely-spaced point habitats were studied over a three-year period in a subtropical area of South Africa. A total of 20,746 individuals in 56 species were sampled with pitfall traps. Rapid species turnover occurred during short periods after longer intervals of relatively constant species composition. There was annual cycling of total numbers of individuals. The temporal variance for total number of individuals within each habitat increased significantly with mean population size by a logarithmic regression. This indicates that population fluctuations are dependent upon the mean, with a distinctive relationship. The total number of species was cyclical, with annual and approximately half-yearly cycles. Each habitat nevertheless carried a characteristic mean number of species. The temporal variance of species richness showed a highly significant positive logarithmic relationship with the mean number of species. Pheidole megacephala (F.) accounted for 45% of all individuals. Its overall population showed annual cycles. Ph. megacephala population trend was the main determinant for seasonal variation of the whole assemblage in most habitats. Percentage dominance was positively linearly correlated with the variance and with mean population level. Although Ph. megacephala population variance increased with the mean, proportionate variability did not, indicating that high populations are no more variable than low populations. Five variability measures were compared with each other on ant assemblages containing only the common species (1st quartile) and then including the increasingly rare species (1st and 2nd, 1st, 2nd and 3rd, and all quartiles). Williamson's Variability Measure, using logarithmic or inverse sine transformations, gave variable results depending whether or not the rarer species were included in the analysis. The Coefficient of Fluctuation also gave variable results depending on assemblage size. The Coefficient of Variation and Proportionate Variability Measure gave similar and consistent results, indicating that common species are not more variable than rare ones. The rarer species are stenotopic and tend always to be rare, whereas the common species are eurytopic, highly competitive and demographically volatile. Control measures for common ants, and conservation of rare ants, should take cognizance of these trends.     

Bryozoan assemblages on hard substrata: species abundance distribution and competition for space

Bryozoans are colonial invertebrates that often dominate epibenthic assemblages on the lower surfaces of hard substrata. Competition among neighbouring organisms is usually a critical process regulating biodiversity, and hard substrata have proved to be a suitable model habitat to analyse spatial interactions. We explored the relationships among abundance, species richness, diversity, competitive ability, coverage, available surface, depth and substratum size in an assemblage of bryozoans encrusting pebbles and cobbles in a bank off the eastern mouth of the Strait of Magellan. We also tested whether overgrowth competition can be regarded as hierarchical, and whether the species abundance distribution shows a mode of rare species and a decreasing frequency of increasingly abundant species. Abundance, species richness, diversity and overgrowth competition were highest on the largest substrata. Smaller pebbles tended to be encrusted by the commonest bryozoans, while the rarest species were mainly found on relatively larger clasts. A high proportion of the lower surfaces of most substrata was available for growth. Diversity values of relatively shallow stations were lower than expected under Caswell’s neutral model. Interspecific competition was hierarchical, but the abundance of colonies was not related to the competitive ability of each species. The species abundance distribution was bimodal, with a main mode of rare species and a second one partly composed of relatively abundant bryozoans with poor competitive abilities. This study shows that even in an encrusting assemblage where competition is hierarchical, the weakest competitors persist and the dominant species are far from being capable of monopolizing space.     

Linking local ecological knowledge and habitat modelling to predict absolute species abundance on large scales

Assessing the spatial structure of abundance of a species is a basic requirement to carry out adequate conservation strategies. However, existing attempts to predict species abundance, particularly in absolute units and on large scales, are scarce and have led to weak results. In this work we present a scheme to obtain, in an affordable way, a predictive model of absolute animal abundance on large scales based on the modelling of data obtained from local ecological knowledge (LEK) and its calibration. To exemplify this scheme, we build and validate a predictive absolute abundance model of the endangered terrestrial tortoise Testudo graeca in Southeast Iberian Peninsula. For that purpose, we collected distribution and relative abundance data of T. graeca using a low cost methodology, such as LEK, by means of interviewing shepherds. The information from LEK was employed to build a predictive habitat-based model of relative abundance. The relative abundance model was transformed into an absolute abundance model by means of calibration with a classical absolute abundance sampling method such as distance sampling. The obtained absolute abundance model predicted the observed absolute abundances values well in independent locations when compared with other works (R ² = 36%) and thus can offer a cost-effective predictive ability. Our results show that reliable habitat-based predictive maps of absolute species abundance on regional scales can be obtained starting from low cost sampling methods of relative abundance, such as LEK, and its calibration.     

Longitudinal patterns of fish assemblages in a large tropical river in southeastern Brazil: evaluating environmental influences and some concepts in river ecology

This study aimed to evaluate environmental influences on fish distribution and to assess the extent to which concepts in river ecology accommodate levels of spatio-temporal heterogeneity of fish assemblages in a 1,080-km long tropical river. A total of 25 sites were sampled between November 2002 and March 2003 in two seasons (summer/wet versus winter/dry). A thermal gradient separating the upper reaches from the lower reaches was detected. The middle-upper reaches showed higher conductivity and lower dissolved oxygen and pH levels compared with the other reaches. Although some significant associations were found between some fish abundance and environmental variables, the most abundant species (Tilapia rendalli, Geophagus brasiliensis, and Oligosarcus hepsetus) occurred in most sites and under most environmental conditions. Fish community structure varied more in space (longitudinal) than through time (seasonal). The community in the lower reach species was more diverse in comparison with the other reaches. Differences in the fish assemblage structure among the longitudinal river sections appear to have been influenced by the effects of damming, and seem to be partially consistent with the Serial Discontinuity Concept, which views dams as discontinuities within the river continuum. Only the lower river reach showed seasonal differences in the fish community structure, attributable to the influence of flooding. Management plans and biodiversity conservation will benefit by considering the effects of dam disruption and flood increased connectivity to the lotic systems. Handling editor: J. Trexler     

Temporal and spatial variation in the long-term functional organization of fish assemblages in a large river

We examined abundances of fishes by ecological categories for variation with time (years) and longitudinal river distance (km) in the Wabash River, a large US Midwestern river. An ordination resulted in significant correlations with time for an axis that represented increases in surface-feeding invertivores and species that prefer sand substrates. We found increased abundances of planktivores and species with high tolerance to silt in downstream river sites. We found significant changes in abundance for the majority of ecological categories in comparisons of upstream–downstream locations. There was a general decrease in abundances of taxa in ecological categories that tend to inhabit upstream reaches: species that prefer rubble substrates, inhabit fast, and moderate current velocity habitats, and that have low silt tolerance with time. These abundance changes suggest that the upstream river experienced increased sedimentation during 1974–1998. The use of ecological categories provided information for likely habitat changes, such as increased sedimentation, that were not apparent in previous taxonomic analyses. We suggest that combinations of anthropogenic impacts including hydrologic alterations and agricultural activities in the Wabash River resulted in ecosystem changes and subsequent changes in abundance of fishes by ecological categories.     

Evaluation of surveillance methods for monitoring house fly abundance and activity on large commercial dairy operations

Relative house fly, Musca domestica L., activity at three large dairies in central California was monitored during the peak fly activity period from June to August 2005 by using spot cards, fly tapes, bait traps, and Alsynite traps. Counts for all monitoring methods were significantly related at two of three dairies; with spot card counts significantly related to fly tape counts recorded the same week, and both spot card counts and fly tape counts significantly related to bait trap counts 1-2 wk later. Mean fly counts differed significantly between dairies, but a significant interaction between dairies sampled and monitoring methods used demonstrates that between-dairy comparisons are unwise. Estimate precision was determined by the coefficient of variability (CV) (or SE/mean). Using a CV = 0.15 as a desired level of estimate precision and assuming an integrate pest management (IPM) action threshold near the peak house fly activity measured by each monitoring method, house fly monitoring at a large dairy would require 12 spot cards placed in midafternoon shaded fly resting sites near cattle or seven bait traps placed in open areas near cattle. Software (FlySpotter; http://ucanr.org/ sites/FlySpotter/download/) using computer vision technology was developed to count fly spots on a scanned image of a spot card to dramatically reduce time invested in monitoring house flies. Counts provided by the FlySpotter software were highly correlated to visual counts. The use of spot cards for monitoring house flies is recommended for dairy IPM programs.     

Mammals' camera-trapping in Sierra Nanchititla, Mexico: relative abundance and activity patterns

Species conservation and their management depend on the availability of their population behavior and changes in time. This way, population studies include aspects such as species abundance and activity pattern, among others, with the advantage that nowadays new technologies can be applied, in addition to common methods. In this study, we used camera-traps to obtain the index of relative abundance and to establish activity pattern of medium and large mammals in Sierra Nanchititla, Mexico. The study was conducted from December 2003 to May 2006, with a total sampling effort of 4 305 trap-days. We obtained 897 photographs of 19 different species. Nasua narica, Sylvilagus floridanus and Urocyon cinereoargenteus were the most abundant, in agreement with the relative abundance index (RAI, number of independent records/100 trap-days), and according to previous studies with indirect methods in the area. The activity patterns of the species showed that 67% of them are nocturnal, except Odocoileus virginianus, Nasua narica and others. Some species showed differences with previously reported patterns, which are related with seasonality, resources availability, organism sex, principally. The applied method contributed with reliable data about relative abundance and activity patterns.     

Microhabitat use by a post-settlement stage estuarine fish: evidence from relative abundance and predation among habitats

Seagrass beds provide food and shelter for many fish species. However, the manner in which fishes use seagrass bed habitats often varies with life stage. Juvenile fishes can be especially dependent on seagrass beds because seagrass and associated habitats (drift macroalgae) may provide an effective tradeoff between shelter from predation and availability of prey. This study addressed aspects of habitat use by post-settlement pinfish, Lagodon rhomboides (Linneaus), an abundant and trophically important species in seagrass beds in the western North Atlantic and Gulf of Mexico. Abundance of post-settlement fish in seagrass beds was positively related to volume of drift macroalgae, but not to percent cover of seagrass, indicating a possible shelter advantage of the spatially complex algae. Tethering experiments indicated higher rates of predation in seagrass without drift macroalgae than in seagrass with drift macroalgae. Aquarium experiments showed lower predation with higher habitat complexity, but differences were only significant for the most extreme cases (unvegetated bottom, highest macrophyte cover). Levels of dissolved oxygen did not differ between vegetated and unvegetated habitats, indicating no physiological advantage for any habitat. Seagrass beds with drift macroalgae provide the most advantageous tradeoff between foraging and protection from predation for post-settlement L. rhomboides. The complex three-dimensional shelter of drift macroalgae provides an effective shelter that is embedded in the foraging habitat provided by seagrass. Drift macroalgae in seagrass beds is a beneficial habitat for post-settlement L. rhomboides by reducing the risk of predation, and by providing post-settlement habitat within the mosaic (seagrass beds) of adult habitat, thus reducing risks associated with ontogenetic habitat shifts.