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.

Peroxidase activity of a TSA-like antioxidant protein from a pathogenic amoeba

The 29 kDa surface protein of Entamoeba histolytica is an abundant antigenic protein expressed by pathogenic strains of this organism. The protein is a member of a widely-dispersed group of homologues which includes at least two cysteinyl peroxidases, Salmonella typhimurium alkyl hydroperoxidase C-22 protein (AhpC) and Saccharomyces cerevisiae thiol-specific antioxidant protein (TSA). Here, for the first time in a pathogenic eukaryote, we have demonstrated that the amoebic protein also possesses peroxidatic and antioxidant activities in the presence of reductants such as dithiothreitol or thioredoxin reductase plus thioredoxin. Although the S. typhimurium AhpF flavoprotein was not an effective reductant of the amoebic TSA protein, one inhibitory monoclonal antibody directed toward amoebic TSA was also partially inhibitory toward reduced but not oxidized bacterial AhpC. These antioxidant proteins are likely to be important not only in general cell protection, but also in the promotion of infection and invasion by these pathogenic organisms through protection against oxidative attack by activated host phagocytic cells.

Luteinizing hormone-releasing hormone in undifferentiated and differentiated SK-N-SH human neuroblastoma cells

The presence of luteinizing hormone-releasing hormone (LHRH) in SK-N-SH human neuroblastoma cells was investigated by immunocytochemistry and enzyme-linked immunosorbent assays of whole cell extracts and culture medium. In addition, ribonuclease protection assays were utilized to quantitate LHRH messenger RNA. The expression of LHRH mRNA and LHRH protein level was correlated with neuronal differentiation induced by retinoic acid (RA). In differentiated SK-N-SH cells the LHRH mRNA level as well as the amount of LHRH in cell extracts and cell medium were significantly lower than in differentiated cells. These results suggest that RA affects the expression of LHRH mRNA and the level of LHRH protein in SK-N-SH cells. These data show that altering the growth state of the human neuroblastoma SK-N-SH cells toward more neuronal phenotype results in a significant decrease in expression of LHRH mRNA and the protein. The ability of RA to induce changes in LHRH at the mRNA and at the peptide levels will allow further study of RA regulation of LHRH at the neuronal level.

Surface localization, regulation, and biologic properties of the 96-kDa alcohol/aldehyde dehydrogenase (EhADH2) of pathogenic Entamoeba histolytica

The 96-kDa surface antigen of Entamoeba histolytica was demonstrated through extensive immunologic evaluation with monoclonal and monospecific antibodies to be identical to or an isoform of the amebic alcohol/aldehyde dehydrogenase (EhADH2). EhADH2 was secreted, excreted, or shed into the culture medium in quantities commensurate with amebic growth when studied in a novel culture system. Of importance, using RNase protection assays, specific mRNA coding for the EhADH2 gene product(s) was up-regulated by treatment of viable trophozoites with the enzyme substrate ethanol. These data provide insight into the biology of this enzyme and its regulation by appropriate stressors.

Serologic reactivity to purified recombinant and native 29-kilodalton peripheral membrane protein of pathogenic Entamoeba histolytica

The 29-kDa peripheral membrane protein of Entamoeba histolytica has recently been demonstrated to have epitopes on pathogenic clinical isolates which were not detected by monoclonal antibodies on nonpathogenic isolates. To analyze the serological response to this protein, we tested 93 serum specimens (from 33 patients with amebic liver abscess, 7 patients with colitis, 2 patients with ameboma, 18 individuals harboring a nonpathogenic zymodeme strain, 10 healthy Mexican migrant workers, and 23 healthy controls) by enzyme-linked immunosorbent assay (ELISA) using immunoaffinity-purified native or recombinant protein. When tested by ELISA with the native antigen, 79% (26 of 33) of the serum specimens from patients with amebic liver abscess, 4 of 9 serum specimens from symptomatic patients with colitis or ameboma, and serum from one migrant worker were positive. None of the 18 subjects harboring a nonpathogenic strain or 23 control individuals were seropositive to the native antigen (sensitivity, 71%; specificity, 98%). Of 30 serum specimens from patients with amebic liver abscess tested with recombinant antigen, 27 were seropositive (90%). In addition, six patients with colitis or ameboma and two individuals who harbored a nonpathogenic strain were seropositive to the recombinant antigen. One healthy Mexican migrant worker tested positive by both ELISAs (sensitivity, 87%; specificity, 94%). Immunoblotting of 51 serum specimens to sodium dodecyl sulfate-denatured native 29-kDa protein was less sensitive (65%) than ELISA in detecting serum antibodies to the antigen. These results suggest a similar antibody response to native and recombinant antigens (r = 0.86) and support the potential utility of a quantitative assay with defined recombinant antigen for the serodiagnosis of invasive amebiasis in nonendemic areas in conjunction with other diagnostic tools.

Structural analysis and demonstration of the 29 kDa antigen of pathogenic Entamoeba histolytica as the major accessible free thiol-containing surface protein

The 29 kDa protein of pathogenic Entamoeba histolytica is a cysteine-rich surface antigen which we recently characterized by cDNA sequencing and by using monoclonal antibodies which differentiated between pathogenic and non-pathogenic clinical isolates. To determine the structure and biochemical attributes of this protein, a repertoire of immunological techniques using monoclonal antibodies, and radiolabelling were employed. We demonstrated that the 29 kDa protein forms a 60 kDa dimer and a high-molecular-mass oligomer(s) on the surface of the organism through disulphide bonds, and is the major accessible free thiol-containing surface protein of E. histolytica. The deduced amino acid sequence encoding the 29 kDa protein was found to share a common amino acid domain with sequences reported for Helicobacter pylori, Salmonella typhimurium, MER5 gene expressed in murine erythroleukemia cells, Clostridium pasteurianum, and a Bacillus spp.

Molecular and cellular characterization of the 29-kilodalton peripheral membrane protein of Entamoeba histolytica: differentiation between pathogenic and nonpathogenic isolates

To further characterize the 29-kDa surface antigen of Entamoeba histolytica, we analyzed the complete nucleotide sequence and compared the immunoreactivity of this antigen in pathogenic and nonpathogenic strains. Five cDNA clones (one 1.0-kb full-length clone, designated p13, and four partial-length clones) encoding the antigen were analyzed for allelic variation. Comparison of the nucleotide sequences revealed several single-nucleotide substitutions in all five cDNAs, two of which resulted in amino acid differences. Localization of the antigen to the amebic surface in a previous report (B. E. Torian, B. M. Flores, V. L. Stroeher, F. S. Hagen, and W. E. Stamm, Proc. Natl. Acad. Sci. USA 87:6358-6362, 1990) was corroborated by transmission electron microscopy showing colloidal gold particles on the surface of the trophozoites. Computer analysis of the deduced amino acid sequence predicted that the protein encoded by p13 was a hydrophilic peripheral membrane protein, and these data were confirmed by a Triton X-114 membrane extraction showing the presence of the 29-kDa antigen primarily in the aqueous phase of the detergent partition. Monoclonal antibodies to a fusion peptide differentiated between pathogenic and nonpathogenic clinical strains of E. histolytica in immunoblots. Although no immunoreactive epitopes were detected on nonpathogenic strains, Northern (RNA) analysis and DNA-DNA hybridization with a 700-bp cDNA probe demonstrated that mRNA and the gene encoding the 29-kDa surface antigen were present in both pathogenic and nonpathogenic clinical isolates.

Experimental infection of pig-tailed macaques (Macaca nemestrina) with Campylobacter cinaedi and Campylobacter fennelliae

Campylobacter cinaedi and C. fennelliae have been associated with proctocolitis, bacteremia, and asymptomatic rectal infection, primarily in homosexual men. To more directly assess the pathogenic role of these organisms, we studied their disease-producing potential in 12- to 25-day-old pig-tailed macaques (Macaca nemestrina). Four infant monkeys were challenged with 10(8) to 10(9) C. cinaedi, three were challenged with C. fennelliae, two were challenged with C. jejuni, and one received no microorganisms. Watery or loose stools without associated fever or fecal leukocytes developed 3 to 7 days postinoculation in all of the animals given C. cinaedi, C. fennelliae, and C. jejuni, but not in the control animal. Stool cultures were simultaneously positive and remained so in the animals challenged with C. cinaedi or C. fennelliae for 3 weeks after inoculation despite the resolution of clinical illness. All of the animals challenged with C. cinaedi and C. fennelliae became bacteremic, and three had clinical evidence of septicemia. Histopathologic evaluation of rectal biopsies (five animals) and necropsy (one animal) showed no evidence of mucosal disruption. Specific immunoglobulin M and immunoglobulin G antibody responses occurred in all of the animals challenged with C. cinaedi and C. fennelliae, as determined by enzyme-linked immunosorbent assay and immunoblotting. We conclude that C. cinaedi and C. fennelliae consistently produce a diarrheal illness accompanied by bacteremia and followed by prolonged gastrointestinal colonization in M. nemestrina.

Differentiation of Naegleria fowleri from Acanthamoeba species by using monoclonal antibodies and flow cytometry

Monoclonal antibodies to Naegleria fowleri and Acanthamoeba polyphaga were analyzed by enzyme-linked immunosorbent assay, indirect immunofluorescence microscopy, and fluorescence flow cytometry to assess specificity and cross-reactivity with axenically cultured N. fowleri and Acanthamoeba spp. Four monoclonal antibodies to N. fowleri were specific for N. fowleri and had no reactivity to A. polyphaga. Similarly, four monoclonal antibodies to A. polyphaga did not react with N. fowleri. Two of the four monoclonal antibodies to A. polyphaga did not react with other Acanthamoeba spp. tested, while two of the antibodies demonstrated a high degree of cross-reactivity with a putative Acanthamoeba castellanii strain by immunofluorescence microscopy; this was confirmed by fluorescence flow cytometry for one of the antibodies. These monoclonal antibodies were used to identify Acanthamoeba trophozoites in infected brain sections of a patient who died of suspected Acanthamoeba-caused granulomatous amoebic encephalitis, demonstrating potential utility in the direct identification of N. fowleri and Acanthamoeba spp. in clinical specimens.

cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica

A gamma gt11 cDNA library was constructed from poly(U)-Sepharose-selected Entamoeba histolytica trophozoite RNA in order to clone and identify surface antigens. The library was screened with rabbit polyclonal anti-E. histolytica serum. A 700-base-pair cDNA insert was isolated and the nucleotide sequence was determined. The deduced amino acid sequence of the cDNA revealed a cysteine-rich protein. DNA hybridizations showed that the gene was specific to E. histolytica since the cDNA probe reacted with DNA from four axenic strains of E. histolytica but did not react with DNA from Entamoeba invadens, Acanthamoeba castellanii, or Trichomonas vaginalis. The insert was subcloned into the expression vector pGEX-1 and the protein was expressed as a fusion with the C terminus of glutathione S-transferase. Purified fusion protein was used to generate 22 monoclonal antibodies (mAbs) and a mouse polyclonal antiserum specific for the E. histolytica portion of the fusion protein. A 29-kDa protein was identified as a surface antigen when mAbs were used to immunoprecipitate the antigen from metabolically 35S-labeled live trophozoites. The surface location of the antigen was corroborated by mAb immunoprecipitation of a 29-kDa protein from surface-125I-labeled whole trophozoites as well as by the reaction of mAbs with live trophozoites in an indirect immunofluorescence assay performed at 4 degrees C. Immunoblotting with mAbs demonstrated that the antigen was present on four axenic isolates tested. mAbs recognized epitopes on the 29-kDa native antigen on some but not all clinical isolates tested.

The 96-kilodalton antigen as an integral membrane protein in pathogenic Entamoeba histolytica: potential differences in pathogenic and nonpathogenic isolates

A surface antigen (EH-96) of Entamoeba histolytica was demonstrated to be a plasma membrane antigen by immunoprecipitation of metabolically 35S-labeled antigen from live trophozoites, Triton X-114 detergent extracts, and plasma membrane-enriched fractions prepared by concanavalin A membrane stabilization and differential centrifugation. In addition, the antigen was localized to the plasma membrane by electron microscopy with colloidal gold. Antigen from E. histolytica strains immunoprecipitated with specific immunoglobulin M (IgM) or IgG2b monoclonal antibody was identical by one-dimensional peptide mapping with N-chlorosuccinimide. Additionally, antigen from different axenically cultivated amebae was demonstrated to be identical by N-chlorosuccinimide peptide mapping, as were peptide maps of IgG and IgM monoclonal antibody-purified antigen. The 96-kilodalton (kDa) surface antigen was identified on four axenically cultivated pathogenic isolates and on three polyxenically cultivated pathogenic isolates (zymodeme II) of E. histolytica but was absent or present in lesser quantity on six nonpathogenic polyxenically cultivated isolates. The 96-kDa antigen was detected in liver abscess fluid from four patients with amebic abscesses by enzyme-linked immunosorbent assay (ELISA) and immunoprecipitation. Two-dimensional gel electrophoresis profiles of the 96-kDa antigen purified from abscess material or from polyxenically cultivated trophozoites demonstrated that the antigens were related to the 96-kDa antigen found in axenically cultivated organisms.

Characterization of Campylobacter cinaedi and C. fennelliae antigens and analysis of the human immune response

Whole-cell protein patterns of Campylobacter cinaedi and C. fennelliae, identified by SDS-PAGE, differed from one another and from five other catalase-positive Campylobacter species. When immunoblotted with rabbit antisera, C. cinaedi and C. fennelliae showed antigenic profiles that were highly species-specific and had little or no cross-reactivity with antigens of the other Campylobacter species tested. Antibody responses of 13 homosexual men with C. cinaedi infection demonstrated consistent reactions with five antigens (96-41 kDa). All human sera tested, including those of 10 culture-negative individuals, reacted with the C. cinaedi 59- and 64-kDa bands, but the overall responses of infected individuals were much stronger. The antigenic profiles of C. cinaedi and C. fennelliae can be used to distinguish these species from other Campylobacter species. At least six C. cinaedi antigens are immunogenic in humans.

Successive bacteremias with "Campylobacter cinaedi" and "Campylobacter fennelliae" in a bisexual male

A bisexual human immunodeficiency virus-seropositive male had successive bacteremias with "Campylobacter cinaedi" and "Campylobacter fennelliae." Because final identification of both isolates was not completed until 1 month after the last admission of the patient, a novel and nonstandardized antimicrobial susceptibility testing method was useful in guiding timely antimicrobial therapy.

Isolation of "Campylobacter hyointestinalis" from a human

We isolated "Campylobacter hyointestinalis" from the rectal culture of a homosexual man with proctitis. Phenotypic characterization of the isolate was confirmed by DNA hybridization by using the taxonomic spot blot. "C. hyointestinalis" was previously isolated only from animals but should be considered in the identification of Campylobacter species isolated from humans.

In vitro susceptibilities of Campylobacter-like organisms to twenty antimicrobial agents

We determined MICs of 20 antimicrobial agents for 50 representative strains of four subgroups of Campylobacter-like organisms (CLOs) by agar dilution. Ampicillin, gentamicin, doxycycline, tetracycline, ceftriaxone, rifampin, spectinomycin, nalidixic acid, and chloramphenicol were active against all strains of CLOs. Most CLO strains (83%) were inhibited by 4 micrograms of sulfamethoxazole per ml and by 8 micrograms of trimethoprim-sulfamethoxazole per ml. Of type 1 strains, 28% were resistant to 8 micrograms of erythromycin per ml. In addition, cross resistance between erythromycin and clindamycin was always present. Type 1 strains exhibited a broad distribution of MICs of metronidazole and streptomycin, whereas all type 2 strains were uniformly susceptible to metronidazole and resistant to streptomycin. Unlike type 1 and 3 strains, type 2 CLOs were susceptible to cephalothin and penicillin G and highly resistant to streptomycin. The type 3 strain was uniquely resistant to cefazolin. The majority of strains were not inhibited by cefoperazone; and all were resistant to trimethoprim. In contrast to Campylobacter jejuni and Campylobacter fetus subsp. fetus, all CLOs tested were susceptible to 0.5 microgram of rifampin per ml.