Genetic structure of traditional varieties of bitter manioc in three soils in Central Amazonia

Manioc is the most important food crop that originated in Amazonia. Many studies have increased our understanding of its evolutionary dynamics under cultivation. However, most of them focused on manioc cultivation in environments with low soil fertility, generally Oxisols. Recent ethnobotanical observations showed that bitter manioc also performs well in high fertility soils, such as Amazonian dark earths (ADE) and the floodplain. We used 10 microsatellite loci to investigate the genetic diversity and structure of bitter manioc varieties grown in different soil types in communities of smallholder farmers along the middle Madeira River in Central Amazonia. The genetic diversity of some sweet varieties and seedlings was also evaluated. Adult individuals showed higher levels of genetic diversity and smaller inbreeding coefficients (A ( R ) = 5.52, H ( O ) = 0.576, f = 0.086) than seedlings (A ( R ) = 4.39, H ( O ) = 0.421, f = 0.242). Bitter manioc varieties from the floodplain showed higher levels of genetic diversity (A ( R ) = 5.19, H ( O ) = 0.606) than those from ADE (A ( R ) = 4.45, H ( O ) = 0.538) and from Oxisols (A ( R ) = 4.15, H ( O ) = 0.559). The varieties grown in the floodplain were strongly differentiated from the varieties grown in Oxisols (F ( ST ) = 0.093) and ADE (F ( ST ) = 0.108), suggesting important genetic structuring among varieties grown in the floodplain and upland soils (ADE and Oxisols). This is the first time that genetic divergence of bitter manioc varieties in cultivation in different Amazonian soils in a small geographic area is reported.     

Microsatellite markers for the cardinal tetra Paracheirodon axelrodi,a commercially important fish from central Amazonia

The cardinal tetra Paracheirodon axelrodi is a very popular aquarium fish and the most important ornamental fishery resource for riverine communities inhabiting the Rio Negro floodplain in central Amazonia. Here we describe the isolation and characterization of 14 microsatellite DNA loci for cardinal tetras. Number of alleles and heterozygosity per locus in a sample of 30 fish ranged from 2 to 22 and from 0.49 to 0.92, respectively. These markers provide powerful tools for studies on conservation and management of cardinal tetra resources and for investigating evolutionary processes underlying population diversification in Amazonian flooded forest fishes.     

Distribution and abundance of tree species in swamp forests of Amazonian Ecuador

Research to date on Amazonian swamps has reinforced the impression that tree communities there are dominated by a small, morphologically specialized subset of the regional flora capable of surviving physiologically challenging conditions. In this paper, using data from a large‐scale tree inventory in upland, floodplain, and mixed palm swamp forests in Amazonian Ecuador, we report that tree communities growing on well‐drained and saturated soils are more similar than previously appreciated. While our data support the traditional view of Amazonian swamp forests as low‐diversity tree communities dominated by palms, they also reveal four patterns that have not been well documented in the literature to date: 1) tree communities in these swamp forests are dominated by a phylogenetically diverse oligarchy of 30 frequent and common species; 2) swamp specialists account for < 10% of species and a minority of stems; 3) most tree species recorded in swamps (> 80%) also occur in adjacent well‐drained forest types; and 4) many tree species present in swamps are common in well‐drained forests (e.g. upland oligarchs account for 34.1% of all swamp stems). These observations imply that, as in the temperate zone, the composition and structure of Amazonian swamp vegetation are determined by a combination of local‐scale environmental filters (e.g. plant survival in permanently saturated soils) and landscape‐scale patterns and processes (e.g. the composition and structure of tree communities in adjacent non‐swamp habitats, the dispersal of propagules from those habitats to swamps). We conclude with suggestions for further research to quantify the relative contributions of these factors in structuring tree communities in Amazonian swamps.     

Fluxes of bacteria and organic matter into a blackwater river from river sediments and floodplain soils

1. The Ogeechee River, in south-eastern Georgia, U.S.A, is a blackwater river with an extensive floodplain that is inundated regularly during winter months. Previous studies have shown that low to moderate bacterial production rates cannot support the relatively high suspended bacteria concentrations observed (10^7?-10⁸ cells ml^?1), suggesting an allochthonous source of bacteria. We report the results of a combination of field and flume experiments which demonstrate that river sediments and floodplain soils are significant sources of suspended bacteria during seasonal flooding. Benthic bacteria are also entrained by normal discharges. There are sizeable fluxes of POC and DOC from river sediments and floodplain soils. 2. Bacterial, POC and DOC fluxes (14, 250, and 790 mg Cm^?2 h^?1, respectively) were substantial when water was percolated upward through floodplain soils. 3. Simulation of overland flow using a flume demonstrated further fluxes of bacteria and POC from floodplain soils (up to 61 and 10700 mg Cm^?2h^?1, respectively) and river sediments, but did not yield additional DOC from floodplain soils. 4. These laboratory results are supported by experiments in which we measured significant increases in concentrations of bacteria and DOC in a downstream direction in (i) the main river channel during a winter flood in 1986, and (ii) a floodplain slough (channel side-arm) which re-entered the main channel 800m from its initial divergence. Inputs of bacteria and DOC from the surrounding floodplain were estimated to be up to 3500 kg DOC h^?1, and 4000 kg bacteria Ch^?1 over a 50-km reach. 5. These previously unmeasured fluxes of organic carbon help to explain the high concentrations of suspended bacteria in the Ogeechee River.     

Fish mediate high food web connectivity in the lower reaches of a tropical floodplain river

High levels of hydrological connectivity during seasonal flooding provide significant opportunities for movements of fish between rivers and their floodplains, estuaries and the sea, possibly mediating food web subsidies among habitats. To determine the degree of utilisation of food sources from different habitats in a tropical river with a short floodplain inundation duration (~2 months), stable isotope ratios in fishes and their available food were measured from three habitats (inundated floodplain, dry season freshwater, coastal marine) in the lower reaches of the Mitchell River, Queensland (Australia). Floodplain food sources constituted the majority of the diet of large-bodied fishes (barramundi Lates calcarifer, catfish Neoarius graeffei) captured on the floodplain in the wet season and for gonadal tissues of a common herbivorous fish (gizzard shad Nematalosa come), the latter suggesting that critical reproductive phases are fuelled by floodplain production. Floodplain food sources also subsidised barramundi from the recreational fishery in adjacent coastal and estuarine areas, and the broader fish community from a freshwater lagoon. These findings highlight the importance of the floodplain in supporting the production of large fishes in spite of the episodic nature and relatively short duration of inundation compared to large river floodplains of humid tropical regions. They also illustrate the high degree of food web connectivity mediated by mobile fish in this system in the absence of human modification, and point to the potential consequences of water resource development that may reduce or eliminate hydrological connectivity between the river and its floodplain.     

Useful Species Richness,Proportion of Exotic Species,and Market Orientation on Amazonian Dark Earths and Oxisols<Superscript>1</Superscript>

Useful Species Richness, Proportion of Exotic Species, and Market Orientation on Amazonian Dark Earths and Oxisols Anthropogenic soils of Amazonia, known as Amazonian Dark Earths (ADE), are environments with elevated soil fertility that can produce crops that otherwise yield poorly on the leached and highly acidic Oxisols that dominate much of the basin. While ADE sites near urban centers often attract commercial horticultural production of nutrient–demanding exotics, these soils are also considered possibly unique reservoirs of endemic agrobiodiversity because of their relationship to pre–Columbian indigenous occupation. Through botanical surveys and interviews with smallholder farmers, this study compared useful species richness, proportion of exotic species, and market orientation of farms situated on ADE and non–anthropogenic Oxisols in the municipality of Borba in Central Brazilian Amazonia. Species richness was similar on Amazonian Dark Earth and Oxisol farms (19.6 spp vs. 18.3 spp); however, ADE farms showed significantly higher proportions of exotic species (39% vs. 26%; p = 0.025). Furthermore, ADE farms in Borba demonstrated significantly higher market orientation (61.0% vs. 47.3%; p = 0.028), likely a result of the advantage of Amazonian Dark Earths for production of crops that are nutrient–demanding or pH–sensitive crops that have higher values in the nearby regional market of Manaus.     

Structure,function and resilience to desiccation of methanogenic microbial communities in temporarily inundated soils of the Amazon rainforest (Cunia Reserve,Rondonia)

The floodplain of the Amazon River is a large source for the greenhouse gas methane, but the soil microbial communities and processes involved are little known. We studied the structure and function of the methanogenic microbial communities in soils across different inundation regimes in the Cunia Reserve, encompassing nonflooded forest soil (dry forest), occasionally flooded Igapo soils (dry Igapo), long time flooded Igapo soils (wet Igapo) and sediments from Igarape streams (Igarape). We also investigated a Transect (four sites) from the water shoreline into the dry forest. The potential and resilience of the CH₄ production process were studied in the original soil samples upon anaerobic incubation and again after artificial desiccation and rewetting. Bacterial and archaeal 16S rRNA genes and methanogenic mcrA were always present in the soils, except in dry forest soils where mcrA increased only upon anaerobic incubation. NMDS analysis showed a clear effect of desiccation and rewetting treatments on both bacterial and archaeal communities. However, the effects of the different sites were less pronounced, with the exception of Igarape. After anaerobic incubation, methanogenic taxa became more abundant among the Archaea, while there was only little change among the Bacteria. Contribution of hydrogenotrophic methanogenesis was usually around 40%. After desiccation and rewetting, we found that Firmicutes, Methanocellales and Methanosarcinaceae became the dominant taxa, but rates and pathways of CH₄ production stayed similar. Such change was also observed in soils from the Transects. The results indicate that microbial community structures of Amazonian soils will in general be strongly affected by flooding and drainage events, while differences between specific field sites will be comparatively minor.     

Hydrologic and geomorphic considerations in restoration of river-floodplain connectivity in a highly altered river system,Lower Missouri River,USA

Planning for restoration of river-floodplain systems requires understanding how often and how much of a floodplain may be inundated, and how likely the floodplain is to retain the water once flooded. These factors depend fundamentally on hydrology and geomorphology of the channel and floodplain. We discuss application of an index of river-floodplain connectivity, the Land Capability Potential Index (LCPI), to regional-scale restoration planning along 600 km of the Lower Missouri River. The LCPI integrates modeled water-surface elevations, floodplain topography, and soils to index relative wetness of floodplain patches. Geomorphic adjustment of the Lower Missouri River to impoundment and channel engineering has altered the natural relations among hydrology, geomorphology, and floodplain soils, and has resulted in a regional upstream to downstream gradient in connectivity potential. As a result, flow-regime management is limited in its capacity to restore floodplain ecosystems. The LCPI provides a tool for identifying and mapping floodplain restoration potential, accounting for the geomorphic adjustment. Using simple criteria, we illustrate the utility of LCPI-like approaches in regional planning for restoration of plains cottonwood (Populus deltoides) communities, hydrologically connected floodplain wetlands, and seasonal floodplain wetlands.     

Central Amazonian floodplain forests: Tree adaptations in a pulsing system

Amazonian floodplain forests are characterized by an annual flood pulse with changes of the water table that exceed 10 meters. Seedlings and adult trees are waterlogged or submerged for continuous periods lasting up to seven months per year. The monomodal flood pulse of the rivers causes drastic changes in the bioavailability of nutrients, oxygen levels, and concentrations of phytotoxins. The aquatic phase occurs during a period in which temperature and light conditions are optimal for plant growth and development, implying the need for adaptations. Not only do trees persist in a dormant state, they grow vigorously during most of the year, including the aquatic period. The regularity of flooding may have enhanced the evolution of specific traits, which partially are well known from floodplain trees in other tropical and in temperate regions. Different kinds of adaptations are found at the level of structural, physiological, and phenological traits. Combinations of adaptations regarding seed germination, seedling development, and traits of roots, shoots, and leaves result in a variety of growth strategies among trees. These lead to specific species distributions and zonations along the flooding gradient and within Amazonian floodplain systems (nutrient-rich white-water várzea and nutrient-poor black-water igapó).     

Effects of the Flooding Gradient on Tree Community Diversity in Várzea Forests of the Purus River,Central Amazon,Brazil

Amazonian floodplain forests have remarkable variation in tree diversity and structure related to flood duration. We assessed how floodplain forests respond to the continuum flooding gradient and found that Fisher's α values vary up to seven times across the landscape.     

Pressurized gas transport in Amazonian floodplain trees

Trees of Central Amazonian whitewater floodplain forests are subjected to extended flood periods lasting several months. They must therefore be highly adapted to long-term flooding and to oxygen shortage in the soil and roots which is expected to be the main stress factor in this environment. The improvement of oxygen transport to the roots by pressurized gas transport, known for some tree species of the temperate zone, is one specific adaptation to flooding. To evaluate its significance, gas transport measurements were carried out under experimental conditions with saplings of five Amazonian tree species. Internal aeration of the roots was improved under conditions of pressurized gas transport as shown by polarographical measurements of oxygen exchange between root and rhizosphere. Tracer gas measurements using sulphur hexafluoride (SF₆) showed gas permeability of transport pathways between stem base and roots. Based on the data, we suppose that pressurized gas transport significantly contributes to internal aeration of roots in Amazonian floodplain saplings growing on the higher levels in the flooding gradient, with low water columns, and is an important adaptation for establishment in these temporarily inundated habitats also in the weeks of rising and lowering water levels.     

Back from the past? Assessment of nitrogen removal ability of buried historic wetland soils before and after a 1-year incubation on a restored floodplain

Stream, floodplain, and wetland restorations enhance water quality and ecological function; however, soil health is prioritized infrequently in restoration planning and monitoring. Buried, historic, hydric soils—common across U.S. mid-Atlantic valley bottoms beneath legacy sediments—are not included in most floodplain restoration designs, though they may retain favorable biogeochemical characteristics and host legacy microbial communities that could support ecosystem recovery if exhumed and preserved. To assess the efficacy of including historic hydric soils in floodplain restoration for nitrogen (N) removal, we characterized pre-Euro-American settlement wetland soils buried below legacy sediments and now exposed along incised streambanks across the mid-Atlantic. We compared carbon (C) and N contents; C:N ratios; nitrate-N and ammonium-N concentrations; denitrification rates; functional genes for denitrification (nosZ) and nitrification (amoA for ammonia oxidizing archaea [AoA] + ammonia oxidizing bacteria [AoB]); and phospholipid fatty acid biomasses of historic wetland soils with contemporary wetland soils before and after an 1-year incubation in a recently restored floodplain. Compared to modern wetland soils, historic hydric soils buried by legacy sediment are less nutrient-rich, have fewer functional genes for and lower rates of denitrification, and possess significantly less microbial biomass. Following the 1-year incubation, many of these concentrations, rates, and gene counts increased in historic soils, though not substantially. Ultimately, our results suggest that while inclusion of historic, hydric soils and their legacy microbiomes is valuable for N-removal in floodplain restoration, the recovery of historic, hydric soils is predictably slow, and attainment of restoration goals, such as increased denitrification, may require multiple years.     

Species richness,composition, and spatial distribution of vascular epiphytes in Amazonian black-water floodplain forests

This study examines the occurrence of vascular epiphytic species in Central Amazonian black-water floodplain forests (igapó) and considers whether their horizontal and vertical distribution is influenced by the flood pulse, as is the case with tree species (phorophytes). Research was conducted in sixteen forest plots the Jaú National Park. In these, epiphytes on all phorophytes with DBH ≥ 10 cm were identified. We measured flood height using the watermark left by the last high-water period, then estimated the height relative to the ground of every epiphytic individual. We recorded 653 individuals in 37 species, distributed on 109 phorophytes. Igapó floodplain forests have much lower richness and abundance of vascular epiphyte species than do other Amazonian forests. This may reflect the limitation of available sites for colonization (only 24.9% of studied trees were occupied by epiphytes). Holoepiphytes predominated, and the combined presence of a flood-pulse, linked to the nutrient-poor soil poor seems to limit the occurrence of nomadic vines. Horizontal distribution of epiphytes followed the distribution of phorophytes, which in turn followed the flood-level gradient. Also flooding interacted strongly with vertical zonation to determine species richness. As already well-reported for trees, and unlike reports of epiphytes in other floodplains, flooding strongly influenced richness and distribution of vascular epiphytes in the studied igapó forests.     

Reconfiguring Agrobiodiversity in the Amazon Estuary: Market Integration, the Açaí Trade and Smallholders’ Management Practices in Amapá, Brazil

An established body of literature documents current changes in rural livelihoods, agricultural practices, and agrobiodiversity patterns in smallholder communities across the globe. Contributing to this literature, this paper documents change in agricultural practices and agrobiodiversity patterns in a tidal floodplain settlement in Amapá, Brazil, where in recent years farmers increasingly devote their attention to the production of açaí fruits, an important regional crop with strong local, national and international markets. Research results indicate that farmers are abandoning subsistence production in annual fields to make room for açaí-dominated agroforests. At the same time, farmers are diversifying home gardens, and as a result conserve a portion of the crop diversity once maintained in annual fields in these areas. Agrobiodiversity documented in home gardens is much higher than previously recorded in the study area, and is equal or higher than previously reported in home gardens in other less-market integrated Amazonian communities. Research points to the need for innovative methods to document agrobiodiversity patterns in today’s modifying landscapes and for the historical analysis of such patterns to avoid presumptions that observed changes are unilateral and unidirectional.     

Heavy Metal Contamination in Sediments and Floodplain Topsoils of the Lean River Catchment,China

Heavy metals (Cd, Ni, Cu, Pb, and Zn) and total sulfur (TS) in both surficial sediments and adjacent floodplain topsoils of the Lean River catchment are investigated to comprehend the effects of flooding on heavy metals in soils, the evolution of the quality of sediments, and transfer of sediment metals. The results show that concentrations of metals except for Ni in soils are significantly correlated with those in sediments. At most upstream or downstream locations, sediment metal concentrations are found comparable to those in soils (sed/soil≈1). For Cu at locations close to the Dexing Copper Mine (DCM), flooding brought Cu-poor clays into the floodplain soil system and this leads to sed/soil<1, while at locations adjacent to the Yinshan Lead-zinc Mine (YLM), suspended solids containing high concentrations of iron and magnesium oxide absorb large quantities of dissolved Cd, Pb, and Zn and deposit on the floodplain during flooding (sed/soil>1). In spite of an elevated Cu production of the DCM, a significant decrease in sediment Cu concentrations is found as compared to those 10 years ago. The decrease may be due to the elevated Cu ore utilizing efficiency and the use of a new modern tailing pool. At the location closest to the Yinshan Lead-zinc Mine (YLM), Pb and Zn concentrations increased in recent sediments. In the Lean River, metal contamination in sediments cannot reach the location 60 km downstream of their sources in 2005.     

Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake

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Nutrient limitation of plant growth on the floodplain of the Narran River, Australia: growth experiments and a pilot soil survey

Water resource development has altered the hydrological regime on the Lower Balonne River in Queensland, Australia. Concerns have been raised about possible impacts to floodplain plant communities, which support a pastoral industry and a range of native fauna. Water and nutrients commonly limit plant growth in south central Queensland, where the climate is semi-arid and the soils are infertile. Floodplain plant productivity is boosted by inundation with water, but the role of flooding in nutrient provision is not known. Growth experiments and a pilot soil survey were conducted to help determine if soil nutrient deficiencies exist and if regular flooding is required to maintain floodplain soil fertility. Soils were sampled from areas representing three flood frequency classes: high, moderate, and low. Chemical extractions were performed as a surrogate for `bioavailable' nutrients. Soil nitrogen (N) but not phosphorus (P) limited the growth of seedlings of wheat (Triticum aestivum L. Gardia) based on responses to nutrient additions: plants supplied with N had greater shoot length and total biomass than plants without N. Clear evidence of an effect of flood frequency on fertility was not revealed. Neither soil P, soil N, nor plant growth varied significantly with flood frequency. However, this analysis had low statistical power. There were trends for greater biomass of seedlings grown on moderately flooded soils and thinner roots for seedlings grown on frequently flooded soils, but neither of these growth responses was clearly linked to nutrient limitation. Nevertheless, the possibility that flooding provides a nutrient subsidy to plants cannot be ruled out because of a number of factors, including the statistical power of this analysis and the possibility that short-term nutrient subsidies occur with floods.     

Three fishes in one: cryptic species in an Amazonian floodplain forest specialist

Accurately describing biodiversity in tropical regions such as Amazonia is difficult because of insufficient morphological inventories and the lack of studies on the distribution of genetic diversity. Aquatic organisms from Amazonian flooded forests are generally expected to move laterally along the forests during the annual inundation cycle, a behaviour that should promote admixture of populations and reduce within‐drainage speciation. We used an unprecedented fine‐scale sampling effort and multiple DNA markers to quantify region‐wide population differentiation in an Amazonian floodplain forest specialist, the black‐wing hatchet fish Carnegiella marthae ( Myers, 1927 ). Our study revealed three previously unsuspected and ancient cryptic species of black‐wing hatchet fish in the Rio Negro floodplain (RNF), in central Amazonia. Two species produce occasional first‐generation hybrids. The third and rarer species, although found in extreme sympatry with another species, appears to be reproductively isolated, and also differs in external morphology and dentition. Our findings have important implications for guiding conservation management because C. marthae is harvested commercially in the RNF ornamental fishery. They also suggest that the diversity of Amazonian ichthyofauna is vastly underestimated, including that found in landscapes lacking contemporary barriers to account for population divergence and speciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 391–403.     

Using river color to predict Amazonian floodplain forest avifaunas in the world's largest blackwater river basin

Despite the importance of rivers in Amazonian biogeography, avian distribution patterns in river‐created habitats (i.e., floodplain forests) have been sparsely addressed. Here, we explore geographic variation in floodplain forest avifaunas, specifically regarding one of the most striking aspects of the Amazon: the diversity of river “colors” (i.e., types, based on the color of the water). We sampled the avifauna at 30 sites, located in 17 different rivers (nine black‐ and eight whitewater), in the Rio Negro basin, northwestern Brazil. Our sampling comprised ten 15‐min point‐counts per site, distributed every 500–1000 m along the river. We recorded a total of 352 bird species, many of which occurred in both river types. Although bird species richness was similar among rivers, we found significant differences in species composition. Nearly 14 percent of the species were significantly associated with one or the other river type. Most floodplain forest specialists occurred predominantly in whitewater rivers, whereas species that are typically associated with white‐sand habitats occurred in blackwater. Despite significant distinctions between river types, occurrence patterns and levels of habitat association differed among indicator species and may vary in the same species throughout its global distribution. There were also “intermediate” avifauna in some of our sites, suggesting that continuous parameters characterizing river types structure species turnover. The water color‐based classification of Amazonian rivers represents a simple and powerful predictor of the floodplain forest avifauna, offering a stimulating starting point for understanding patterns of floodplain bird distributions and for prioritizing conservation efforts in these overlooked habitats. Abstract in Portuguese is available with online material.     

Influence of market orientation on food plant diversity of farms located on Amazonian Dark Earth in the region of Manaus, Amazonas, Brazil

Homegardens may serve as reservoirs of agro-biodiversity on highly fertile, anthropogenic Amazonian Dark Earth (ADE) soils of the Amazon basin. However, as these soils are used more intensively for market-oriented agriculture, we suspected a decrease in their agro-biodiversity. We present data obtained from surveys on 16 farms where ADE was present in the region of Manaus, Amazonas, Brazil. When farms were separated into two groups by market orientation, species richness on the farms was not significantly influenced by market orientation, but there was less dominance (i.e., more diversity) for homegardens in the low-market orientation group (P < 0.1). The proportion of native species was not affected by market orientation. Hence, while the most market-oriented farms retained high species richness, homegardens located on them contained higher proportions of commercially interesting species.