Patterns in the Composition of Microbial Communities from a Subtropical River: Effects of Environmental,Spatial and Temporal Factors

Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO₄-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NO_x-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.     

Temporal and Spatial Distribution Patterns of Larval Trichoptera in Madeiran Streams

Temporal and spatial distribution patterns of lotic larval trichopteran assemblages in relation to environmental variables were investigated in Madeiran streams using multivariate analyses. TWINSPAN classification detected distinct faunal assemblages related to spatial factors between non-polluted high altitude sites and lower lying enriched sites where tolerant taxa were predominant but showed strong seasonal shifts in species composition and abundance. The 15 TWINSPAN end groups were grouped into five arbitrary clusters based upon the seasonal and spatial changes in the trichopteran assemblages detected by the analysis. Significant differences between environmental variables (distance from source, altitude, temperature, conductivity, alkalinity and nitrate) and the trichopteran assemblages (using trichopteran based metrics) of these clusters were confirmed by the Kruskal-Wallis test (H) and Dunn’s test. Chemical classification of samples within the clusters revealed a strong association between trichopteran assemblages and water quality. Canonical Correspondence Analysis and Monte Carlo global permutation tests also identified significant associations between the larval assemblages and physicochemical variables such as temperature and conductivity along a strong physical gradient (altitude, slope) and nitrate along a weaker seasonal gradient. Analysis of functional feeding group distribution patterns clearly showed that mid to high altitude indigenous woodland sites were trophically diverse whilst the lower reaches of the islands streams are trophically impoverished with strong seasonal shifts between two feeding groups of enrichment tolerant taxa. Trichopteran shredders are exclusive to indigenous woodland sites, indicating a limited distribution associated with land use, allochthonous input and habitat destruction. The results indicate that several ‘environmental filters’ operate at different levels upon the islands trichopteran fauna, producing temporally and spatially distinct ‘subsets’ of species best able to exploit conditions and resources at a given site or time, confounding the direct comparison of these insular systems with the findings of the River Continuum Concept, traditionally associated with unaffected continental lotic systems.     

Spatial and Temporal Patterns in Assemblages of Temperate Reef Fish

SYNOPSIS. For reef fish in temperate marine regions, such componentsof local assemblage diversity (i.e., within a reef) as speciesrichness, total fish density, and rank order of abundance canremain relatively constantthrough time. Long-term data (17 years)for assemblages on 2 reefs in Southern California revealed that,despite high turnover in rare species, overall species richnesswas affected only moderately by major oceanographicdisturbances.This resilience of the assemblage is in marked contrast to hightemporal variation in densities exhibited by many local populationsof individual species, and it suggests that measurements ofdiversity to indicate status of an assemblage should be usedwith caution. Here we consider various processes and factors,together with the spatial and temporal scales over which theyoperate, that can influence local diversity (and its estimation)of reef fishes. Mechanisms that can "buffer" local diversityof reef fishes include dispersal of young that inter-connectssubpopulations, high "inertia" in relative abundance and populationstructures (especially for long-lived species), and broad ecologicalrequirements of many species. These considerations suggest thatthe effect of disturbances on local diversity of reef fisheswill depend in part on the magnitude, duration, frequency andspatial scale of the perturbation. While long-term data arefew, available information suggests that, due to life historycharacteristics of the fish and the spatial and temporal scalesat which disturbances are likely to occur, assemblages of temperatemarine reef fish might be relatively resilient to environmentalperturbations     

Spatiotemporal Variation in Shallow-Water Freshwater Fish Distribution and Abundance in a Large Subtropical Coastal Lagoon

Patos Lagoon is located off the southern Brazilian coast and represents one of the largest coastal lagoons in the world. We estimated hydrological and physicochemical conditions associated with spatial variation in the abundance and diversity of freshwater fishes along the lagoon, and inter-annual variability in abundances of freshwater fishes occurring in its estuarine zone. During our study, the region experienced two periods of average rainfall and two periods with above-average rainfall. The characids Astyanax eigenmaniorum and Oligosarcus jenynsii and the siluriform Parapimelodus nigribarbis were the most abundant freshwater fishes in the estuary during wet periods when water levels were higher and salinity was lower. Increases in abundance of these species in the estuarine area, all of which members of primary-division freshwater families, apparently were associated with pulses of reproduction and passive transport from freshwater habitats located near middle and upper lagoon reaches. Abundance of species from secondary freshwater families, such as poeciliids and cichlids, were less correlated with hydrological conditions, and their patterns of occurrence in the estuary suggest active migration from nearby freshwater habitats draining into this area. Findings indicate that freshwater discharge in the basin and expansion/retraction of freshwaters in the middle-upper lagoon determined patterns of freshwater fish abundance and species richness in the estuarine zone.     

Patterns of Occurrence of Sharks in Sydney Harbour,a Large Urbanised Estuary

Information about spatial and temporal variability in the distribution and abundance of shark-populations are required for their conservation, management and to update measures designed to mitigate human-shark interactions. However, because some species of sharks are mobile, migratory and occur in relatively small numbers, estimating their patterns of distribution and abundance can be very difficult. In this study, we used a hierarchical sampling design to examine differences in the composition of species, size- and sex-structures of sharks sampled with bottom-set longlines in three different areas with increasing distance from the entrance of Sydney Harbour, a large urbanised estuary. During two years of sampling, we obtained data for four species of sharks (Port Jackson, Heterodontus portusjacksoni; wobbegong, Orectolobus maculatus; dusky whaler, Carcharhinus obscurus and bull shark, Carcharhinus leucas). Only a few O. maculatus and C. obscurus were caught, all in the area closest to the entrance of the Harbour. O. maculatus were caught in all seasons, except summer, while C. obscurus was only caught in summer. Heterodontus portusjacksoni were the most abundant species, caught in the entrance location mostly between July to November, when water temperature was below 21.5°C. This pattern was consistent across both years. C. leucas, the second most abundant species, were captured in all areas of Sydney Harbour but only in summer and autumn when water temperatures were above 23°C. This study quantified, for this first time, how different species utilise different areas of Sydney Harbour, at different times of the year. This information has implications for the management of human-shark interactions, by enabling creation of education programs to modify human behaviour in times of increased risk of potentially dangerous sharks.     

Origin of Fish Biomass in a Diverse Subtropical River: An Allochthonic-Supported Biomass Increase Following Flood Pulses

Ecosystems - The origin of resources supporting metazoan biomass in rivers has long been a subject of debate. The river wave concept (RWC) postulates that the energetic basis of food webs varies...     

Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions.     

Shift in a Large River Fish Assemblage: Body-Size and Trophic Structure Dynamics

As the intensity and speed of environmental change increase at both local and global scales it is imperative that we gain a better understanding of the ecological implications of community shifts. While there has been substantial progress toward understanding the drivers and subsequent responses of community change (e.g. lake trophic state), the ecological impacts of food web changes are far less understood. We analyzed Wabash River fish assemblage data collected from 1974-2008, to evaluate temporal variation in body-size structure and functional group composition. Two parameters derived from annual community size-spectra were our major response variables: (1) the regression slope is an index of ecological efficiency and predator-prey biomass ratios, and (2) spectral elevation (regression midpoint height) is a proxy for food web capacity. We detected a large assemblage shift, over at least a seven year period, defined by dramatic changes in abundance (measured as catch-per-unit-effort) of the dominant functional feeding groups among two time periods; from an assemblage dominated by planktivore-omnivores to benthic invertivores. There was a concurrent increase in ecological efficiency (slopes increased over time) following the shift associated with an increase in large-bodied low trophic level fish. Food web capacity remained relatively stable with no clear temporal trends. Thus, increased ecological efficiency occurred simultaneous to a compensatory response that shifted biomass among functional feeding groups.     

Seasonality of a Floodplain Subsidy to the Fish Community of a Large Temperate River

Ecosystems - This study examines the temporal and spatial variability of the floodplain trophic contribution to the fish community of Lake Saint-Pierre, a large (≈ 300 km2),...     

Transfer and Occurrence of Large Mercury Resistance Plasmids in River Epilithon

In situ mating experiments were done in the River Taff, South Wales, United Kingdom, by using a natural mercury resistance plasmid (pQM1) isolated from a mixture of epilithic bacteria in vitro. The river temperature from March to November was found to influence transfer frequencies strongly (6.8 × 10⁻⁹ to 1.5 × 10⁻² per recipient). A linear relationship existed between log₁₀ transfer frequency and river temperature (6 to 21°C), a 2.6°C change in temperature giving a 10-fold change in transfer frequency. In vitro experiments showed that pQM1 transferred most efficiently between fluorescent pseudomonads and that one epilithic isolate (Pseudomonas fluorescens) was an efficient donor in situ. Experiments with a P. putida recipient showed that intact epilithic bacterial communities could transfer mercury resistance plasmids in situ at frequencies of up to 3.75 × 10⁻⁶ per recipient. Nineteen of the large (>250-kilobase) plasmids isolated by transfer into P. putida were studied in detail and grouped into seven types by restriction digests. Mercury resistance and UV resistance were found to be common linked phenotypes in 19 of the 23 plasmids tested.     

Contrasting Patterns of Larval Mortality in Two Sympatric Riverine Fish Species: A Test of the Critical Period Hypothesis

Understanding the causal mechanisms that determine recruitment success is critical to the effective conservation of wild fish populations. Although recruitment strength is likely determined during early life when mortality is greatest, few studies have documented age-specific mortality rates for fish during this period. We investigated age-specific mortality of individual cohorts of two species of riverine fish from yolksac larvae to juveniles, assaying for the presence of a “critical period”: A time when mortality is unusually high. Early life stages of carp gudgeons (Hypseleotris spp.) and unspecked hardyhead (Craterocephalus stercusmuscarum fulvus)—two fishes that differ in fecundity, egg size and overlap between endogenous and exogenous feeding—were collected every second day for four months. We fitted survivorship curves to 22 carp gudgeon and 15 unspecked hardyhead four-day cohorts and tested several mortality functions. Mortality rates declined with age for carp gudgeon, with mean instantaneous mortality rates (-Z) ranging from 1.40–0.03. In contrast, mortality rates for unspecked hardyhead were constant across the larval period, with a mean -Z of 0.15. There was strong evidence of a critical period for carp gudgeon larvae from hatch until 6 days old, and no evidence of a critical period for unspecked hardyhead. Total larval mortality for carp gudgeon and unspecked hardyhead up to 24 days of age was estimated to be 97.8 and 94.3%, respectively. We hypothesise that life history strategy may play an important role in shaping overall mortality and the pattern of mortality during early life in these two fishes.     

Flowering and Fruiting Patterns in a Subtropical Rain Forest,Taiwan

Reproductive patterns of tropical and temperate plants are usually associated with climatic seasonality, such as rainfall or temperature, and with their phylogeny. It is still unclear, however, whether plant reproductive phenology is influenced by climatic factors and/or phylogeny in aseasonal subtropical regions. The plant reproductive phenology of a subtropical rain forest in northern Taiwan (24°45′ N, 121°35′ E) was monitored at weekly intervals during a 7‐yr period (2002–2009). The flowering patterns of 46 taxa and fruiting patterns of 26 taxa were examined and evaluated in relation to climatic seasonality, phylogenetic constraints, and different phenophases. Our results indicated that most of the studied species reproduced annually. Additionally, both community‐wide flowering and fruiting patterns exhibited distinct annual rhythms and varied little among years. The community flowering peak matched seasonal changes in day length, temperature, and irradiance; while the community fruiting peak coincided with an increase in bird richness and the diet‐switching of resident omnivorous birds. In addition, phylogenetically closely related species tended to reproduce during the same periods of a year. Neither the mean flowering dates nor seasonal variation in solar radiation, however, was related to the fruit development times. Our results indicate the importance of abiotic, biotic, and evolutionary factors in determining the reproductive phenology in this subtropical forest.     

Effects of Landscape and Riparian Condition on a Fish Index of Biotic Integrity in a Large Southeastern Brazil River

Environmental conditions of a large river in southeastern Brazil were assessed by evaluating fish assemblage structure (index of biotic integrity, IBI), landscape use (forest, pasture, urban area, and tributary water) and riparian condition. A survey of the 338 km-long middle reach of the Rio Paraiba do Sul, containing a large urban-industrial complex, was conducted in two seasons: summer/wet and winter/dry. Fish were sampled with a standardized level of effort twice at seven sites, between March 2001 and April 2002, by gill nets, cast nets, sieves and seines. Riparian condition was evaluated by direct observations, and land use maps were used to assess landscape condition of an 8 km² buffer surrounding each site. IBI scores ranged from 5 to 36 (out of a possible range of 4–40), with lowest values at an urban-industrial landscape, and highest scores upstream and downstream, indicating the river’s recovery capacity. The most appropriate time to assess IBI was during the winter/dry period, when sampling was more effective and the IBI was more sensitive to changes in environmental quality. Landscape use and riparian condition were correlated, and IBI was positively correlated with % pasture, % tributary area, and riparian condition, but negatively correlated with % urban area. In some cases urban areas eliminated riparian woody vegetation, destabilizing site physical habitat structure.     

Temporal and Spatial Occurrence of Female Chinook Salmon Carrying a Male-Specific Genetic Marker in the Columbia River Watershed

Recent declines in many chinook salmon, Oncorhynchus tshawytscha, populations within the Columbia River watershed have prompted an examination of their reproductive biology. In a previous study many female fall chinook salmon collected in 1999 from the Hanford Reach of the Columbia River tested positive for a male-specific DNA marker (OtY1) found on the Y chromosome. The purpose of this study was to determine if females testing positive for the OtY1 marker could be found in other populations of fall chinook salmon from the Columbia River, and to assess the prevalence of OtY1 incidence in different female cohorts. Post-spawned male and female fall chinook salmon from three different naturally spawning populations (Hanford Reach, Yakima River and Ives Island) and one hatchery population (Priest Rapids Hatchery) on the Columbia River were tested in 2000 and 2001 for the OtY1 marker. Among naturally spawning populations, 57.4% of the females tested positive from the Hanford Reach, 33.3% tested positive from the Yakima River, and 32.5% tested positive from Ives Island. Of the Priest Rapids Hatchery fish, 62.5% of the females tested positive, and significant differences were detected between the 1995–1996 and 1997–1998 female cohorts from this population. No significant differences were detected between any of the female cohorts from the naturally spawning populations. All male chinook salmon samples, tested positive for OtY1.     

Occurrence of Plant Growth Inhibitors in Tropical and Subtropical Vegetation

Acetone, ethanol and water extracts of mature fruits of yaupon (llex vomitoria Ait.) inhibited germination of mesquite (Prosopis juliflora Swartz DC. var. glandulosa (Torr.) Cockerell and sorghum (Sorghum bicolor (L.) Moench). Extracts of guava fruit (Psidium guajava L.) inhibited cucumber (Cucumis sativus L.) seed germination. Water soluble inhibitors were found in fruits, leaves, roots and bark of several tropical species representing 10 different families. Strong inhibition of cucumber seed germination and growth did not occur in sand when water extracts containing inhibitors were applied. Growth of corn, sorghum, cucumber and bean was reduced in soils collected beneath Malay apple (Eugenia malaccensis L.) trees. Plant growth-inhibitors occurred in all species studied in various plant parts, and some apparently affect the growth and ecology of other plant species.     

Empirical Assessment of Fish Introductions in a Subtropical Wetland: An Evaluation of Contrasting Views

We summarized data from eight quantitative fish surveys conducted in southern Florida to evaluate the distribution and relative abundance of introduced fishes across a variety of habitats. These surveys encompassed marsh and canal habitats throughout most of the Everglades region, including the mangrove fringe of Florida Bay. Two studies provided systematically collected density information over a 20-year period, and documented the first local appearance of four introduced fishes based on their repeated absence in prior surveys. Those species displayed a pattern of rapid population growth followed by decline, then persistence at lower densities. Estuarine areas in the southern Everglades, characterized by natural tidal creeks surrounded by mangrove-dominated marshes, and canals held the largest introduced-fish populations. Introduced fishes were also common, at times exceeding 50% of the fish community, in solution holes that serve as dry-season refuges in short-hydroperiod rockland habitats of the eastern Everglades. Wet prairies and alligator ponds distant from canals generally held few individuals of introduced fishes. These patterns suggest that the introduced fishes in southern Florida at present may not be well-adapted to persist in freshwater marshes of the Everglades, possibly because of an interaction of periodic cold-temperature stress and hydrologic fluctuation. Our analyses indicated low densities of these fishes in central or northern Everglades wet-prairie communities, and, in the absence of experimental data, little evidence of biotic effects in this spatially extensive habitat. There is no guarantee that this condition will be maintained, especially under the cumulative effects of future invasions or environmental change.     

Occurrence and Structure of Iron Inclusions in Adipocytes of Larval Lampreys

The occurrence and structure of adipocytes in the larvae of two lamprey species, Geotria australis and Petromyzon marinus, were examined by electron microscopy. Adipocytes from both species possessed large electron-dense inclusions which histochemical and energy dispersal X-ray analyses show as containing iron. The greatest concentration of inclusions in adipocytes was found in the nephric fold of G. australis. While some iron is present in the cytoplasmic matrix as ferritin, the majority is seen in large ammocoetes in membrane-bound dense aggregations of haemosiderin. The wide variety of inclusion types seen in smaller larvae may reflect on the method of formation of these inclusions within the cell. Because of the high level of iron loading in the larval lamprey nephric fold, this readily accessible tissue may provide a valuable model for studies of iron metabolism in vertebrates.     

Migratory Patterns of Wild Chinook Salmon Oncorhynchus tshawytscha Returning to a Large,Free-Flowing River Basin

Upriver movements were determined for Chinook salmon Oncorhynchus tshawytscha returning to the Yukon River, a large, virtually pristine river basin. These returns have declined dramatically since the late 1990s, and information is needed to better manage the run and facilitate conservation efforts. A total of 2,860 fish were radio tagged during 2002–2004. Most (97.5%) of the fish tracked upriver to spawning areas displayed continual upriver movements and strong fidelity to the terminal tributaries entered. Movement rates were substantially slower for fish spawning in lower river tributaries (28–40 km d^-1) compared to upper basin stocks (52–62 km d^-1). Three distinct migratory patterns were observed, including a gradual decline, pronounced decline, and substantial increase in movement rate as the fish moved upriver. Stocks destined for the same region exhibited similar migratory patterns. Individual fish within a stock showed substantial variation, but tended to reflect the regional pattern. Differences between consistently faster and slower fish explained 74% of the within-stock variation, whereas relative shifts in sequential movement rates between “hares” (faster fish becoming slower) and “tortoises” (slow but steady fish) explained 22% of the variation. Pulses of fish moving upriver were not cohesive. Fish tagged over a 4-day period took 16 days to pass a site 872 km upriver. Movement rates were substantially faster and the percentage of atypical movements considerably less than reported in more southerly drainages, but may reflect the pristine conditions within the Yukon River, wild origins of the fish, and discrete run timing of the returns. Movement data can provide numerous insights into the status and management of salmon returns, particularly in large river drainages with widely scattered fisheries where management actions in the lower river potentially impact harvests and escapement farther upstream. However, the substantial variation exhibited among individual fish within a stock can complicate these efforts.     

Patterns of Fish Use and Piscivore Abundance within a Reconnected Saltmarsh Impoundment in the Northern Indian River Lagoon, Florida

Nearly all saltmarshes in east-central, Florida were impounded for mosquito control during the 1960s. The majority of these marshes have since been reconnected to the estuary by culverts, providing an opportunity to effectively measure exchange of aquatic organisms. A multi-gear approach was used monthly to simultaneously estimate fish standing stock (cast net), fish exchange with the estuary (culvert traps), and piscivore abundance (gill nets and bird counts) to document patterns of fish use in a reconnected saltmarsh impoundment. Changes in saltmarsh fish abundance, and exchange of fish with the estuary reflected the seasonal pattern of marsh flooding in the northern Indian River Lagoon system. During a 6-month period of marsh flooding, resident fish had continuous access to the marsh surface. Large piscivorous fish regularly entered the impoundment via creeks and ditches to prey upon small resident fish, and piscivorous birds aggregated following major fish movements to the marsh surface or to deep habitats. As water levels receded in winter, saltmarsh fish concentrated into deep habitats and emigration to the estuary ensued (200% greater biomass left the impoundment than entered). Fish abundance and community structure along the estuary shoreline (although fringed with marsh vegetation) were not analogous to marsh creeks and ditches. Perimeter ditches provided deep-water habitat for large estuarine predators, and shallow creeks served as an alternative habitat for resident fish when the marsh surface was dry. Use of the impoundment as nursery by transients was limited to Mugil cephalus Linnaeus, but large juvenile and adult piscivorous fish used the impoundment for feeding. In conclusion, the saltmarsh impoundment was a feeding site for piscivorous fish and birds, and functioned as a net exporter of forage fish to adjacent estuarine waters.