Diversity of Entamoeba spp. in African great apes and humans: an insight from Illumina MiSeq high-throughput sequencing

Understanding the complex Entamoeba communities in the mammalian intestine has been, to date, complicated by the lack of a suitable approach for molecular detection of multiple variants co-occurring in mixed infections. Here, we report on the application of a high throughput sequencing approach based on partial 18S rDNA using the Illumina MiSeq platform. We describe, to our knowledge, for the first time, the Entamoeba communities in humans, free-ranging western lowland gorillas and central chimpanzees living in the Dja Faunal Reserve in Cameroon. We detected 36 Entamoeba haplotypes belonging to six haplotype clusters, containing haplotypes possessing high and low host specificity. Most of the detected haplotypes belonged to commensal Entamoeba, however, the pathogenic species (Entamoeba histolytica and Entamoeba nuttalli) were also detected. We observed that some Entamoeba haplotypes are shared between humans and other hosts, indicating their zoonotic potential. The findings are important not only for understanding the epidemiology of amoebiasis in humans in rural African localities, but also in the context of wild great ape conservation.     

Characterization of animal communities involved in seed dispersal and predation of Guibourtia tessmannii (Harms) J.Léonard,a species newly listed on Appendix II of CITES

Characterization of the ecology of endangered timber species is a crucial step in any forest management strategy. In this study, we described the animal communities involved in seed dispersal and predation of a high‐value timber species Guibourtia tessmannii (Fabaceae; Detarioideae), which is newly listed on Appendix II of CITES. We compared the animal communities between two forest sites (Bambidie in Gabon and Ma'an in Cameroon). A total of 101 hr of direct observations and 355 days of camera trapping revealed that a primate (Cercopithecus nictitans nictitans) and a hornbill (Ceratogymna atrata) were important seed dispersers in Gabon. Conversely, a greater presence of a rodent (Cricetomys emini), which could act both as predator and disperser, was observed in Cameroon. This study suggests that animal communities involved in seed dispersal of G. tessmannii may vary depending on environmental conditions and anthropogenic impacts. However, further studies are needed to properly identify the factors involved in seed dispersal and predation of G. tessmannii.     

Dendrochronological analyses and climatic signals of Alchornea triplinervia in subtropical forest of southern Brazil

The predominance of secondary forest‐species in Brazilian subtropical forests highlights the importance of understanding the ecology of these taxa, and dendrochronology provides valuable information about the growth and climate response of tree species. The wide distribution of Alchornea triplinervia (Spreng.) Mull. Arg. (Euphorbiaceae), and the presence of growth rings in its wood, leds to its selection for this study. Samples were collected from 34 trees growing in rainy dense forest fragments in the cities of Blumenau and Brusque, in southern Brazil, and subjected to standard dendrochronological techniques. The local chronology spanned from 1889 to 2013 and the age of the trees ranged from 32 to 125 years. The mean age was 73 years and annual increment was 1.13 mm year^?1; the diameter and age showed a weak correlation. The results suggest that A. triplinervia growth responded negatively to hot summers and increased rainfall in the previous spring and winter. The high perdiodicity trend characteristic of ENSO activity was reflected in wavelet power spectra of A. triplinervia chronology, affecting positively its growth after strong ENSO events (1970–2009). Negative influences occurred before 1970 during normal ENSO events. Also, there is evidence of the existence of a connection between Pacific and Atlantic sea surface temperatures influencing on tree growth.     

Distribution of stream macroalgae in the eastern Atlantic Rainforest of São Paulo State, southeastern Brazil

Fifty-two stream segments were sampled from 16 August to 13 September in 1993 in the eastern Atlantic Rainforest of S?o Paulo State, southeastern Brazil (22°55′–25°00′S, 44°48′–48°03′W). Forty-two macroalgal subgeneric taxa were found and the most widespread species were Audouinella pygmaea (21% of sites), Compsopogon leptoclados and Microcoleus subtorulosus (19%). Macroalgal species number per sampling site ranged from 0 to six (2.6 ± 1.7) and was positively correlated to species abundance, whereas species cover ranged from 0 to 70% of the stream bed (15.5 ± 20.8%). No significant correlation was found among macroalgal species number and abundance with any physical or chemical variable analyzed. Most sites were dominated by one or few macroalgal species, mainly, Audouinella macrospora, C. leptoclados and M. subtorulosus. No significant difference was found between the frequency distribution of variables measured for streams and for total macroalgae but the most widespread species (A. pygmaea) differed significantly for current velocity, specific conductance, turbidity and pH. Overall means for macroalgal occurrence include the following values: temperature (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiwaaaa!36CA!\[X\] = 19.9°C), current velocity (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiwaaaa!36CA!\[X\] = 45 cm s⁻¹), oxygen saturation (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiwaaaa!36CA!\[X\] = 66%), specific conductance (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiwaaaa!36CA!\[X\] = 59.6 μS cm⁻¹), turbidity (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiwaaaa!36CA!\[X\] = 5 NTU) and pH (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiwaaaa!36CA!\[X\] = 7.1). This pattern of patchy distribution and dominance by few species has been suggested as typical of stream macroalgal communities and has been ascribed to the rapid fluctuation of physical and chemical conditions. Total macroalgal species richness as well as mean species number per sampling site were considerably lower than found in similar studies of other regions. The Intermediate Disturbance Hypothesis was applied to explain these results: the same factor (high precipitation) responsible for the maintainance of the high species diversity in the surrounding forest can be, paradoxically, a constraint to the development of a more diverse macroalgal flora in streams.     

Acclimation of leaf carotenoid composition and ascorbate levels to gradients in the light environment within an Australian rainforest

The influence of the growth photon flux density (PFD) on the size and composition of the carotenoid pool and the size of the reduced ascorbate pool was determined across a light gradient from the forest floor to the canopy and the forest edge of a sub-tropical rainforest in New South Wales, Australia. Nineteen plant species (most collected from multiple sites) representing a broad taxonomic range consistently possessed larger total carotenoid pools when found growing in more exposed sites. There was a significant positive correlation between β-carotene content and growth PFD and a significant negative correlation between α-carotene content and growth PFD. Neoxanthin content exhibited no significant trend while the trend in lutein content varied with mode of expression. The pigments of the xanthophyll cycle (violaxanthin, antheraxanthin and zeaxanthin) exhibited the most pronounced response to growth PFD; they comprised a much greater portion of the total carotenoid pool in high light-acclimated plants. The pool of reduced ascorbate was also several-fold greater in high light-acclimated plants. These acclimatory changes in carotenoid and ascorbate content are consistent with a need for a greater capacity to dissipate excessive absorbed light energy in high light-acclimated plants.     

Nitrate reduction in sediments of lowland tropical streams draining swamp forest in Costa Rica: An ecosystem perspective

Nitrate reduction and denitrification were measured in swamp forest streams draining lowland rain forest on Costa Rica's Atlantic slope foothills using the C₂H₂-block assay and sediment-water nutrient fluxes. Denitrification assays using the C₂H₂-block technique indicated that the full suite of denitrifying enzymes were present in the sediment but that only a small fraction of the functional activity could be expressed without adding NO₃ ^–. Under optimal conditions, denitrification enzyme activity averaged 15 nmoles cm^–3 sediment h^–1. Areal NO₃ ^– reduction rates measured from NO₃ ^– loss in the overlying water of sediment-water flux chambers ranged from 65 to 470 umoles m^–2 h^–1. Oxygen loss rates accompanying NO₃ ^– depletion averaged 750 umoles m^–2 h^–1. Corrected for denitrification of NO₃ ^– oxidized from NH₄ ⁺ in the sediment, gross NO₃ ^– reduction rates increase by 130 umoles m^–2 h^–1, indicating nitrification may be the predominant source of NO₃ ^– for NO₃ ^– reduction in swamp forest stream sediments. Under field conditions approximately 80% of the increase in inorganic N mass along a 1250-m reach of the Salto River was in the form of NO₃ ^– with the balance NH₄ ⁺ . Scrutiny of potential inorganic N sources suggested that mineralized N released from the streambed was a major source of the inorganic N increase. Despite significant NO₃ ^– reduction potential, swamp forest stream sediments appear to be a source of inorganic N to downstream communities.     

Effects of removal and regeneration of bankside vegetation on fish population dynamics in the Warta River,Poland

In March 1989 both banks of a 450 m section of the Warta River, 2 km above a reservoir, were cleared of their riparian vegetation (osiers, willows and alders). In October 1988 17 fish species had been recorded there, with a standing crop (SC) of 31.9 kg ha ^–1. In April 1989, the number of species decreased to 11, and their SC to 7.9 kg ha ^–1.Over the next three years new alder trees appeared and osiers regrew to 3.5 m. The SC in October 1990, October 1991 and May 1992 was recorded at 36.5, 66.2 and 40.9 kg ha ^–1, respectively. The primary effect was on phytophils, whose biomass was directly proportional to the height of the trees and osiers (r = 0.87, p = 0.05). The litho-phytophils appeared to occupy the habitat vacated by the phytophils soon after bank clearance (r = –0.87, p = 0.05), but then declined as the osiers grew.     

A simple calibrated model of Amazon rainforest productivity based on leaf biochemical properties

A simple ‘big leaf’ ecosystem gas exchange model was developed, using eddy covariance data collected at an undisturbed tropical rainforest in south-western Amazonia (Brazil). The model used mechanistic equations of canopy biochemistry combined with an empirical stomatal model describing responses to light, temperature and humidity. After calibration, the model was driven using hourly data from a weather station at the top of the tower at the measurement site, yielding an estimate of gross primary productivity (annual photosynthesis) in 1992/1993 of about 200 mol C m^?2 year ^?. Although incoming photon flux density emerged as the major control on photosynthesis in this forest, at a given PAR CO₂ assimilation rates were higher in the mornings than in the afternoons. This was attributable to stomatal closure in the afternoon in response to increasing canopy-to-air vapour pressure differences. Although most morning gas exchange was clearly limited by the rate of electron transport, afternoon gas exchange was generally observed to be very nearly co-limited by both Rubisco activity (V_max) and electron transport rate. The sensitivity of the model to changes in nitrogen allocation showed that the modelled ratio of V_max to electron transport (J_max) served nearly to maximize the annual carbon gain, and indeed, would have resulted in almost maximum annual carbon gain at the pre-industrial revolution atmospheric CO₂ concentration of 27 Pa. Modelled gross primary productivity (GPP) was somewhat lower at 27 Pa, being about 160 mol C m^?2 year^?1. The model suggests that, in the absence of any negative feedbacks on GPP, future higher concentrations of atmospheric CO₂ will continue to increase the GPP of this rainforest, up to about 230 mol C m^?2 year^?1 at 70 Pa.     

Evaluation of the heat pulse velocity technique for measurement of sap flow in rainforest and eucalypt forest species of south-eastern Australia

Sap flow in the stems of two cut saplings each of Eucalyptus maculata (a canopy eucalypt forest tree), Doryphora sassafras and Ceratopetalum apetalum (both canopy rainforest trees of south-eastern coastal Australia) was measured by the heat pulse velocity technique and compared with water uptake from a potometer. Scanning electron micrographs of wounding caused by implantation of temperature sensor and heater probes into the sapwood showed that wounding was similar in rainforest and eucalypt species and was elliptical in shape. A circular wound has been implicitly assumed in previous studies. Accurate measurements of sapling water use were obtained using the smaller transverse wound dimension rather than the larger longitudinal dimension because maximum disruption of sap flow through the xylem vessels occurred in the transverse plane. Accurate measurements of sap flux were obtained above a minimum threshold sap velocity. These velocities were 15·7,10·9 and 9·4 cm h^?1 for E. maculata, C. apetalum and D. sassafras, respectively. Below the threshold sap velocity, however, sap flow could not be accurately calculated from measurements of heat pulse velocity. The minimum threshold sap velocity appeared to be determined by probe construction and xylem anatomy. Despite the elliptical wounding and inaccurate measurement of sap flow below the threshold sap velocity, total sap flow over the experimental period for two saplings of each species was within 7% of water use measured by the potometer.     

Munmarlary revisited: Response of a north Australian Eucalyptus tetrodonta savanna protected from fire for 20 years

Abstract A comparison was made between the total density of tree species recorded on three 1 ha plots that have been protected from fire for 20 years, and from three surrounding sites that have been subjected to the ambient fire regime. Both unburnt plots and ambient sites were in a lowland coastal Eucalyptus tetrodonta savanna in Kakadu National Park. Fire protection resulted in a substantial increase in the number of saplings (16 times more than ambient), poles (five times more than ambient) and trees (2. 5 times more than ambient), but slightly fewer (7%) sprouts than ambient. Of the 32 species recorded in the six 0. 2 ha samples, only nine species could legitimately be analysed using Chi-squared analysis to test for differences in the density of sprouts and saplings between unburnt and ambient samples; eight of these species had significantly different distributions. Typically the unburnt samples had a greater number of saplings compared to ambient conditions, but fewer sprouts. Eucalyptus miniata showed no significant difference in the density of sprouts and saplings between the unburnt and ambient samples. Chi-squared analyses of the frequency distribution among four size classes (sprouts, saplings, poles and trees) was possible for six species. The results for five of these species mirrored the findings of the comparison between sprouts and saplings. However, the fan palm Livistona humilus, which typically forms a component of the mid-layer in E. tetrodonta savannas, was found to have a large number of sprouts on the unburnt samples and a complete absence of stems in any of the other size classes. Dead L. humilus stems attested to the former occurrence of larger size classes of this species on the unburnt plots. No rainforest species were recorded in the unburnt samples. Minor differences in species composition between unburnt and ambient samples are thought to reflect sampling effects. The results of this study are consistent with the conclusions of an earlier study at the same site which also concluded that rainforest tree species do not readily colonize unburnt Eucalyptus savanna.