Globally significant changes in biological processes of the Amazon Basin: results of the Large-scale Biosphere–Atmosphere Experiment

The Amazon River, its huge basin, and the changes in biological processes that are rapidly occurring in this region are unquestionably of global significance. Hence, Global Change Biology is delighted to host a special thematic issue devoted to the Large‐scale Biosphere–Atmosphere Experiment in Amazônia (LBA), which is a multinational, interdisciplinary research program led by Brazil. The goal of LBA is no less modest than its subject: to understand how Amazônia functions as a regional entity in the Earth system and how these functions are changing as a result of ongoing changes in land use. This compilation of 26 papers resulting from LBA‐related research covers a broad range of topics: forest stocks of carbon (C) and nitrogen (N); fluxes of greenhouse gases and volatile organic compounds from vegetation, soils and wetlands; mapping and modeling land‐use change, fire risk, and soil properties; measuring changes caused by logging, pasturing and cultivating; and new research approaches in meteorology to estimate nocturnal fluxes of C from forests and pastures. Some important new synthesis can be derived from these and other studies. The aboveground biomass of intact Amazonian forests appears to be a sink for atmospheric carbon dioxide (CO₂), while the wetlands and soils are a net source of atmospheric methane (CH₄) and nitrous oxide (N₂O), respectively. Land‐use change has, so far, had only a minor effect on basin‐wide emissions of CH₄ and N₂O, but the net effect of deforestation and reforestation appears to be a significant net release of CO₂ to the atmosphere. The sum of the 100‐year global warming potentials (GWP) of these annual sources and sinks of CH₄, N₂O, and CO₂ indicate that the Amazonian forest–river system currently may be nearly balanced in terms of the net GWP of these biogenic atmospheric gases. Of course, large uncertainties remain for these estimates, but the papers published here demonstrate tremendous progress, and also large remaining hurdles, in narrowing these uncertainties in our understanding of how Amazônia functions as a regional entity in the Earth system.     

The Amazon River as a dispersal barrier to passerine birds: effects of river width, habitat and taxonomy

Aim To evaluate the relative effectiveness of the lower and upper sections, respectively, of the Amazon River as a barrier to bird distribution, and to evaluate ecological and taxonomic factors affecting the efficacy of the river barrier. Location Amazon River of South America between its confluence with the Napo River in the west and its delta in the east. Methods Using published distribution maps for 448 species of passerine birds occurring along the Amazon River, we evaluated whether each was distributed along one bank only (river presumed to be a barrier) or both banks (no barrier) to test the predictions that the river was more effective as a dispersal barrier: (1) along the lower, wider portion of the river than the upper, narrower portion; (2) for species inhabiting forests than open country; (3) for species inhabiting forest understorey than forest canopy; (4) for species restricted to terra firme (never inundated upland forest) than those not restricted to terra firme and (5) for certain taxonomic groups. Results Our analyses demonstrated that the Amazon River was most effective as a dispersal barrier along its lower portion and for species restricted to forests and terra firme. However, the river was not significantly more of a barrier for species inhabiting forest understorey than forest canopy. The river was most significant as a barrier to dispersal for the antbirds (Thamnophilidae) and was less significant as a barrier to species belonging to several large families including woodcreepers (Dendrocolaptidae), ovenbirds (Furnariidae), flycatchers (Tyrannidae), cotingids (Cotingidae), tanagers (Thraupidae), seed‐eating finches (Emberizidae) and blackbirds (Icteridae). Main conclusions The robust widths of Amazonian rivers are widely considered to represent impediments to dispersal and gene flow for many taxa of birds and other animals, and may have represented agents of vicariance in the diversification of species. Our study reaffirms the effectiveness of the lower Amazon River as a current barrier to bird dispersal for forest birds and provides new insights into the effects of habitat and taxonomy on the efficacy of the river barrier. Although supportive of several predictions of the river hypothesis of biological diversification, our study is limited in addressing the historical impact of river barriers as agents of vicariance in the process of diversification.     

Characterization of a broad range antibacterial substance from a new <Emphasis Type="Italic">Bacillus</Emphasis> species isolated from Amazon basin

A Bacillus sp. strain producing a bacteriocin-like substance was characterized by biochemical profiling and 16S rDNA sequencing. The phylogenetic analysis indicated that this strain has low sequence similarity with most Bacillus spp., suggesting a new species was isolated. The antimicrobial activity was detected starting at the exponential growth phase, and maximum activity was observed at stationary phase. The substance was inhibitory to a broad range of indicator strains, incluing pathogenic and food spoilage bacteria such as Listeria monocytogenes, B. cereus, Aeromonas hydrophila, Erwinia carotovora, Pasteurella haemolytica, Salmonella Gallinarum, among other. The antibacterial substance was stable over a wide pH range, but it was sensitive to pronase E and lipase. The antibacterial substance was bactericidal and bacteriolytic to L. monocytogenes and B. cereus at 160 AU ml⁻¹. The identification of a broad range bacteriocin-like inhibitory substance active against L. monocytogenes addresses an important aspect of food protection against pathogens and spoilage microorganisms.     

Floodplain connectivity, disturbance and change: a palaeoentomological investigation of floodplain ecology from south-west England

1. Floodplain environments are increasingly subject to enhancement and restoration, with the purpose of increasing their biodiversity and returning them to a more 'natural' state. Defining such a state based solely upon neoecological data is problematic and has led several authors to suggest the use of a palaeoecological approach. 2. Fossil Coleopteran assemblages recovered from multiple palaeochannel fills in south-west England were used to investigate past floodplain and channel characteristics during the mid- to late-Holocene. Ordination of coleopteran data was performed using Detrended Correspondence Analysis (DCA) and produced clear and discrete clustering. This clustering pattern is related to the nature of the environment in which assemblages were deposited and hence channel configuration and dynamics. 3. The DCA clustering pattern is strongly related to measures of ecological evenness, and a strong relationship between these indices and the composition of the water beetle assemblage within samples was revealed. Repeating the ordination with presence-absence data results in a similar pattern of clustering, implying that assemblage composition is crucial in determining cluster placement. 4. As assemblage composition is primarily a function of floodplain topography and hence disturbance regime, we attempt to relate these data to the Intermediate Disturbance Hypothesis (IDH). A significant positive correlation was found between ecological diversity (Shannon's H') and Axis 1 of all ordinations in predominantly aquatic assemblages.     

Floodplain lake fish assemblages in the Amazon River: directions in conservation biology

The Neotropical region is renowned for its high biodiversity, and the Amazon River basin contains the highest number of fish species of any river system in the world. In recent years, habitat fragmentation and exploitation of biotic resources have threatened biological integrity and provoked to need for sustainable management and conservation of the Amazon River system. We studied 36 floodplain lakes along 2000 km of the Amazon River. The fish assemblages associated with flood forests are moderately diverse, with low species dominance and reduced populations. To detect nestedness of fish assemblage composition in floodplain lakes, a nested subset analysis was performed on species presence–absence. The incidence matrix (species × lakes) was maximally packed using the Nestedness Temperature Calculator software. The results of ranking lakes and species allow us to establish targets for conservation. Such strategy for sustainable management should be focused on maintaining the Amazonian biodiversity.     

Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna

The phylogenetic relationships within the piranhas were assessed using mitochondrial sequences with the aim of testing several hypotheses proposed to explain the origin of Neotropical diversity (palaeogeography, hydrogeology and museum hypotheses). Sequences of the ribosomal 16S gene (510 bp) and control region (980 bp) were obtained from 15 localities throughout the main South American rivers for 21 of the 28 extant piranha species. The results indicate that the genus Serrasalmus is monophyletic and comprises three major clades. The phylogeographical analyses of these clades allowed the identification of five vicariant events, extensive dispersal and four lineage duplications suggesting the occurrence of sympatric speciation. Biogeographical patterns are consistent with the prediction made by the museum hypothesis that lineages from the Precambrian shields are older than those from the lowlands of the Amazon. The vicariant events inferred here match the distribution of the palaeoarches and several postdispersal speciation events are identified, thereby matching the predictions of the palaeogeography and hydrogeology hypotheses, respectively. Molecular clock calibration of the control region sequences indicates that the main lineages differentiated from their most recent common ancestor at 9 million years ago in the proto Amazon-Orinoco and the present rate of diversification is the highest reported to date for large carnivorous Characiformes. The present results emphasize that an interaction among geology, sea-level changes, and hydrography created opportunities for cladogenesis in the piranhas at different temporal and geographical scales.     

Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters

Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO₂ outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a complex microbial consortium could explain the quick turnover of TeOM previously observed in this ecosystem.     

An overview of malaria transmission from the perspective of Amazon Anopheles vectors

In the Americas, areas with a high risk of malaria transmission are mainly located in the Amazon Forest, which extends across nine countries. One keystone step to understanding the Plasmodium life cycle in Anopheles species from the Amazon Region is to obtain experimentally infected mosquito vectors. Several attempts to colonise Ano- pheles species have been conducted, but with only short-lived success or no success at all. In this review, we review the literature on malaria transmission from the perspective of its Amazon vectors. Currently, it is possible to develop experimental Plasmodium vivax infection of the colonised and field-captured vectors in laboratories located close to Amazonian endemic areas. We are also reviewing studies related to the immune response to P. vivax infection of Anopheles aquasalis, a coastal mosquito species. Finally, we discuss the importance of the modulation of Plasmodium infection by the vector microbiota and also consider the anopheline genomes. The establishment of experimental mosquito infections with Plasmodium falciparum, Plasmodium yoelii and Plasmodium berghei parasites that could provide interesting models for studying malaria in the Amazonian scenario is important. Understanding the molecular mechanisms involved in the development of the parasites in New World vectors is crucial in order to better determine the interaction process and vectorial competence.     

Species–area relationship within benthic habitat patches of a tropical floodplain river: An experimental test

The curvilinear relationship between species richness and habitat area (species–area relationship (SAR)) is a fundamental ecological pattern. The relationship is often viewed from a long‐term perspective across relatively large spatial scales, reflecting a balance between immigration and extinction dynamics. We explored whether predictions of SAR also manifest over short time periods (days) in benthic habitat patches of a dynamic floodplain river where littoral faunal assemblages are continuously assembled and disassembled with changing water levels. We examined the relationship of patch size with faunal abundance (i.e. fish and aquatic invertebrates), taxonomic richness, trophic group richness and overall assemblage composition. Strong taxa–area relationships emerged despite the relatively short experimental time period (21 days); larger patches had more taxa and trophic groups. For the smallest patches, taxonomic richness was especially sensitive to abundance of individuals; abundance of individuals was a less important predictor of taxonomic and trophic group richness for the largest patches. Despite the relatively short time frame for study within this temporally dynamic ecosystem, our findings indicate a strong SAR for fishes and macroinvertebrates inhabiting patchy habitats in the littoral zone of this tropical river.     

Light and ultrastructural description of Meglitschia mylei n. sp. (myxozoa) from Myleus rubripinnis (Teleostei: Serrasalmidae) in the Amazon River system

Meglitschia mylei n. sp. found in the gall bladder of the teleostean fish Myleus rubripinnis (Serrasalmidae) from the middle Amazonian region of Brazil is described using light and transmission electron microscopy. The spores observed in the bile averaged 24.6±0.8 μm long, 8.7±0.4 μm wide and 5.1±0.3 μm thick and were strongly furcate and arcuate ∩-shaped composed of two symmetric equal-sized valves, up to ～70 nm thick. Each valve possessed one opposed tapering appendage, 20.1±0.7 μm long, oriented parallel towards the basal tip of the appendages and joined along a right suture line forming a thick strand. The strand goes around the central part of the spore, which in turn surrounds two equal and symmetric spherical polar capsules (PC), 2.1±0.3 μm in diameter, located at the same level. Each capsule contains a polar filament with five (rarely six) coils. The binucleate sporoplasm was irregular in shape, contained several sporoplasmosomes, ～175 nm in diameter and filled all the space of the two caudal appendages. Based on the arc shape of the spore with two tapering caudal appendages oriented to the basis of spores, on the number and position of the PC and of the polar filament coils and arrangements, and on the host specificity, we propose the name M. mylei n. sp. for this new myxozoan. Accordingly, this is the second described species of this genus.