One sixth of Amazonian tree diversity is dependent on river floodplains

Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.

Consistent patterns of common species across tropical tree communities

Trees structure the Earth's most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1-6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth's 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world's most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.

Mapping density, diversity and species-richness of the Amazon tree flora

Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.

More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia

Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.

Biased-corrected richness estimates for the Amazonian tree flora

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

Rarity of monodominance in hyperdiverse Amazonian forests

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such “monodominant” forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Study of the occurrence and ecosystem danger of selected endocrine disruptors in the urban water cycle of the city of Bogotá, Colombia

Endocrine disruptors have been studied for their high occurrence in different environments including aquatic; however, in the context of developing countries, their occurrence, magnitude and potential threat have little information. This study involved the analysis of various components of the urban water cycle in the city of Bogotá, Colombia. As a result, it was found that the compounds with the highest occurrence are plasticizers such as phthalates and bisphenol A, whereas among the drugs, carbamazepine presented the highest concentrations (0.68-31.45 µg L^-1); the analysis of the threat coefficient (HQ) showed the importance of bis(2-ethylhexyl) phthalate (BEHP) and estrone (E1) that can reach surface waters from domestic and industrial discharges.

Species Distribution Modelling: Contrasting presence-only models with plot abundance data

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species’ area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.

Estimating the global conservation status of more than 15,000 Amazonian tree species

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world's >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

Hyperdominance in the Amazonian tree flora

The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.

Long-term colonization of spinal cord injury patients with Klebsiella pneumoniae

The duration of colonization of the human perineum, bowel, and urethra with Klebsiella pneumoniae was studied in 10 male patients with spinal cord injury while they were undergoing rehabilitation in the hospital. Colonization defined as persistence of klebsiellae of the same serotype occurred on 13 occasions in five of the patients for up to 55 days. Colonization was less marked with Klebsiella than with Pseudomonas spp. The presence of quadriplegia correlated with Klebsiella colonization and also with the presence of positive Klebsiella cultures from the urethra and perineum. Seven episodes of significant bacteriuria occurred with or after the finding of positive cultures from body sites.

Effect of antiseptic agents on skin flora of the perineum of men with spinal cord injury

Male patients with spinal cord injury are frequently colonized with P. aeruginosa and K. pneumoniae on the perineum. Regular bathing with bar soap has not influenced this colonization. We have attempted to remove these bacteria using antiseptic agents. The number of P. aeruginosa, K. pneumoniae and total aerobic bacteria on the perineum and the penile shaft was determined before and after cleaning with bar soap, chlorhexidine, povidone-iodine and pHresh. Povidone-iodine and chlorhexidine had no advantage over bar soap or pHresh in the removal of P. aeruginosa or K. pneumoniae from the perineum of patients with spinal cord injury.

Pseudomonas aeruginosa colonization in patients with spinal cord injuries

The prevalence of Pseudomonas aeruginosa colonization of patients with spinal cord injury was studied annually from 1976 to 1980. The urethra, perineum, rectum, drainage bag, and urine of patients on the spinal cord injury service were cultured. A total of 224 men and 32 women were studied. Most patients were managed with an external urinary collection system or padding, with or without intermittent catheterization. P. aeruginosa was cultured from one or more body sites (urethra, perineum, or rectum) in 65% of men and 18% of women. Drainage bags on the beds were frequently colonized with P. aeruginosa (73%). Significant bacteriuria with P. aeruginosa was present in 19% of the men and 13% of the women. P. aeruginosa colonization of body sites in men was closely associated with the use of an external urinary collection system. Significantly greater urethral and perineal colonization was found in men using an external urinary collection system. P. aeruginosa serotype 11 was the predominant serotype for the first 3 years, and the number of patients colonized with serotype 11 increased with length of hospital stay. The prevalence of serotype 11 significantly decreased in the last 2 years. The antibiotic susceptibility of the strains of P. aeruginosa isolated from these patients did not change in the 5 years, except that there was increasing susceptibility to carbenicillin in later years. This increasing susceptibility to carbenicillin was a reflection of a decreased prevalence of serotype 11 in these patients, since serotype 11 was more resistant than other serotypes to carbenicillin.

Effects of bathing on Pseudomonas and Klebsiella colonization in patients with spinal cord injuries

This study of Pseudomonas aeruginosa and Klebsiella pneumoniae colonization in humans with spinal cord injuries who were using the external urinary collection system showed that meticulous bathing with the bar soap issued by the hospital did not eliminated colonization and was frequently associated with the shifting of these bacteria to adjacent sites on the body. Bacterial counts of the skin showed that bathing did reduce the numbers of P. aeruginosa and K. pneumoniae found on the skin surface and temporarily eliminated these bacteria from some sites. The persistence of these organisms for long periods, even when patients were meticulously bathed, indicates that P. aeruginosa and K. pneumoniae may become part of the resident flora in these patients.

Selective medium for isolation of Klebsiella pneumoniae

Selective media for Klebsiella pneumoniae have been important in studies of hospital-acquired infections. On an agar medium which included ornithine, raffinose, and Koser citrate, K. pneumoniae strains grew as yellow mucoid colonies at 24 h and there was some increase in colony size at 48 h. Other members of Enterobacteriaceae were inhibited or produced small pink colonies on this same medium. Pseudomonas, Providencia, Acinetobacter, and Proteus species did not grow or showed very poor growth. The growth and appearance of these bacteria were not influenced by pH changes over a pH range of 5.2 to 6.4. Of 368 swabs of body sites cultured on MacConkey agar and on the test medium, 121 K. pneumoniae isolates on MacConkey agar and the same number on the test medium resulted. There were no discrepancies between the two media. Upon direct plating of stool, however, more K. pneumoniae colonies were isolated on the test medium than on MacConkey agar. Colonies on the test medium were more readily selected and identified than the colonies on MacConkey agar. There was also no inhibition of K. pneumoniae growth on the test medium compared with blood agar medium. This medium may be useful for the selective isolation of K. pneumoniae.

Short-course aminoglycoside therapy in patients with spinal cord injury. Standard dose versus low dose

Twenty-nine patients with spinal cord injury and asymptomatic urinary tract infection were treated with standard or reduced doses of tobramycin and amikacin. The patients received five days of intramuscular antibiotics. Most of the patients in the tobramycin groups had Pseudomonas aeruginosa infection and most of those in the amikacin group had either Proteus rettgeri or Providencia stuartii infections. Only 1 patient had a positive urine antibody coating test. High antibiotic concentrations were demonstrated in the urine of all patients during therapy. Urine cultures were obtained two and seven days after completion of therapy. Forty-eight per cent of the patients were cured, while 31 per cent showed persistence or relapse, and 21 per cent had reinfection with other bacteria. No significant differences in results were observed between the standard-dose and low-dose regimens and between the amikacin and tobramycin groups. The low success rate of the regimens used may indicate the need to evaluate alternative therapeutic regimens to treat urinary tract infections in this special group of patients.