Extinction risks of Amazonian plant species

Tree species occurring in Amazonian wetland forests consistently show broader range sizes and niche breadths than trees in upland forests

Generally, species with broad niches also show large range sizes. We investigated the relationship between hydrological niche breadth and geographic range size for Amazonian tree species seeking to understand the role of habitat specialization to Amazonian wetlands and upland forests on the current distribution of tree species. We obtained 571,092 valid occurrence points from GBIF and SpeciesLink to estimate the range size and the niche breadth of 76% of all known Amazonian tree species (5150 tree species). Hydrological niche breadth was measured on different unidimensional axes defined by (1) total annual precipitation; (2) precipitation seasonality; (3) actual evapotranspiration; and (4) water table depth. Geographic range sizes were estimated using alpha-hull adjustments. General linear models were used to relate niche breadth to range size while contrasting tree species occurring and not occurring in wetlands. The hydrological niche breadth of Amazonian tree species varied mostly along the water table depth axis. The average range size for an Amazonian tree species was 751,000 km2 (median of 154,000 km2 and standard deviation of 1,550,000 km2). Niche breadth-range size relationships for Amazonian tree species were positive for all models, and the explanatory power of the models improved when including whether a species occurred in wetlands or in terrestrial uplands. Wetland species had steeper positive slopes for the niche breadth-range size relationship, and consistently larger range sizes for a given niche breadth. Amazonian tree species varied strongly in hydrological niche breadth and range size, but most species had narrow niche breadths and range sizes. Our results suggest that the South American riverscape may have been acting as a corridor for species dispersal in the Neotropical lowlands.

Population Status of a Regionally Endangered Plant, Lunaria rediviva (Brassicaceae), near the Eastern Border of Its Range

Long-term studies of plant populations provide valuable knowledge on the influence of various environmental factors on plant species. The status of edge-range species populations is especially important to be studied due to their higher vulnerability to extinction. This paper aimed to study the Lunaria rediviva population at the eastern border of its range (National Park "Smolny", Republic of Mordovia, Russia). The study was carried out in 2013-2018. Assessment of the L. rediviva population was performed on the basis of individual parameters of plants (height of the individual, number of leaves per individual, number of inflorescences, flowers, fruits per one generative individual, and the fruit set), and density of individuals. Ontogenetic structure of the population was identified by distinguishing juvenile, mature vegetative, and reproductive individuals. The relationships between weather conditions (mean values of temperature, air moisture, wind strength, precipitation divided to three decades per month) and population parameters of L. rediviva were identified. Results showed changes in the ontogenetic structure of the population. The type of its population changed from vegetatively oriented to bimodal, with a decrease (R² = 0.686) in the proportion of mature vegetative individuals. We demonstrated a significant decline in some parameters of the L. rediviva reproduction. We found a significant negative correlation between the fruit set and the moisture at mid-July (r = -0.84, p < 0.05), and wind strength in late May (r = -0.83, p < 0.05) and early June (r = -0.83, p < 0.05). It was found that the number of both flowers and fruits per individual is significantly positively correlated with the precipitation in late April, and they negatively correlated with these parameters and the temperature in late July. We assume that the habitat shading negatively influences the L. rediviva population status.

Mega-dams and extreme rainfall: Disentangling the drivers of extensive impacts of a large flooding event on Amazon Forests

Extreme weather events and the presence of mega-hydroelectric dams, when combined, present an emerging threat to natural habitats in the Amazon region. To understand the magnitude of these impacts, we used remote sensing data to assess forest loss in areas affected by the extreme 2014 flood in the entire Madeira River basin, the location of two mega-dams. In addition, forest plots (26 ha) were monitored between 2011 and 2015 (14,328 trees) in order to evaluate changes in tree mortality, aboveground biomass (AGB), species composition and community structure around the Jirau reservoir (distance between plots varies from 1 to 80 km). We showed that the mega-dams were the main driver of tree mortality in Madeira basin forests after the 2014 extreme flood. Forest loss in the areas surrounding the reservoirs was 56 km² in Santo Antônio, 190 km² in Jirau (7.4–9.2% of the forest cover before flooding), and 79.9% above that predicted in environmental impact assessments. We also show that climatic anomalies, albeit with much smaller impact than that created by the mega-dams, resulted in forest loss along different Madeira sub-basins not affected by dams (34–173 km²; 0.5–1.7%). The impact of flooding was greater in várzea and transitional forests, resulting in high rates of tree mortality (88–100%), AGB decrease (89–100%), and reduction of species richness (78–100%). Conversely, campinarana forests were more flood-tolerant with a slight decrease in species richness (6%) and similar AGB after flooding. Taking together satellite and field measurements, we estimate that the 2014 flood event in the Madeira basin resulted in 8.81–12.47 ∙ 10⁶ tons of dead biomass. Environmental impact studies required for environmental licensing of mega-dams by governmental agencies should consider the increasing trend of climatic anomalies and the high vulnerability of different habitats to minimize the serious impacts of dams on Amazonian biodiversity and carbon stocks.

Tree Communities in Three-Year-Old Post-Mining Sites Under Different Forest Restoration Techniques in the Brazilian Amazon

Forest loss and degradation in the Brazilian Amazon due to mining activities has been intense for many years. To reverse this situation, a range of restoration programs for deforested and degraded areas have been created and implemented. The aim of this study was to analyze the tree composition, successional stage, dispersal and pollination syndromes, conservation status of tree species, and proximity to seed sources under different forest restoration techniques (seedling planting, natural regeneration, and assisted natural regeneration or nucleation) implemented in post-mining sites in the Paragominas municipality (Pará, Brazil). Sixty permanent plots with a restoration age of three years were selected for tree sampling. A total of 119 species, 83 genera and 27 botanical families were identified. Sites restored with different techniques significantly differed in tree composition. Seedling planting sites exhibited the highest abundance, species richness, and diversity values. These were dominated less by pioneer species when compared to the natural regeneration and nucleation sites. Entomophilic pollination and zoochory dispersal were highly represented in the three types of restored sites. Abundance and species richness were negatively correlated with distance from plots to seed sources, and they sharply declined in natural regeneration and nucleation plots at >250 m from seed sources. Four threatened species were identified in the restored sites. We conclude that a combination of different restoration strategies at three-year-old post-mining restoration sites in the Brazilian Amazon results in the recovery of considerable levels of local tree diversity.

Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

Safety margins and adaptive capacity of vegetation to climate change

Vegetation is composed of many individual species whose climatic tolerances can be integrated into spatial analyses of climate change risk. Here, we quantify climate change risk to vegetation at a continental scale by calculating the safety margins for warming and drying (i.e., tolerance to projected change in temperature and precipitation respectively) across plants sharing 100 km × 100 km grid cells (locations). These safety margins measure how much warmer, or drier, a location could become before its 'typical' species exceeds its observed climatic limit. We also analyse the potential adaptive capacity of vegetation to temperature and precipitation change (i.e., likelihood of in situ persistence) using median precipitation and temperature breadth across all species in each location. 47% of vegetation across Australia is potentially at risk from increases in mean annual temperature (MAT) by 2070, with tropical regions most vulnerable. Vegetation at high risk from climate change often also exhibited low adaptive capacity. By contrast, 2% of the continent is at risk from reductions in annual precipitation by 2070. Risk from precipitation change was isolated to the southwest of Western Australia where both the safety margin for drier conditions in the typical species is low, and substantial reductions in MAP are projected.

Is local trait variation related to total range size of tropical trees?

The reasons why the range size of closely related species often varies significantly have intrigued scientists for many years. Among other hypotheses, species with high trait variation were suggested to occupy more diverse environments, have more continuity in their distributions, and consequently have larger range sizes. Here, using 34 tree species of lowlands tropical rainforest in southern Costa Rica, we explored whether inherent trait variability expressed at the local scale in functional traits is related to the species’ total geographical range size. We formed 17 congeneric pairs of one narrow endemic and one widespread species, sampled 335 individuals and measured eight functional traits: leaf area, leaf thickness, leaf dry matter content, specific leaf area, leaf nitrogen content, leaf phosphorus content, leaf nitrogen to phosphorus ratio, and wood specific gravity. We tested whether there are significant differences in the locally expressed variation of individual traits or in multidimensional trait variance between the species in congeneric pairs and whether species’ range size could hence be predicted from local trait variability. However, we could not find such differences between widely distributed and narrow range species. We discuss the possible reasons for these findings including the fact that higher trait variability of widespread species may result from successive local adaptations during range expansion and may hence often be an effect rather than the cause of larger ranges.

Amazon plant diversity revealed by a taxonomically verified species list

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

Evolutionary patterns of range size, abundance and species richness in Amazonian angiosperm trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. The drivers of this variation are not well understood. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to contribute to explaining the variation. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics; closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species. Our results suggest that phylogenetically correlated intrinsic factors, namely traits of the genera themselves, shape among lineage variation in range size, abundance and species richness. We postulate that tree stature may be one particularly relevant trait. However, other traits may also be relevant, and our study reinforces the need for ambitious compilations of trait data for Amazonian trees. In the meantime, our study shows how large-scale phylogenies can help to elucidate, and contribute to explaining, macroecological and macroevolutionary patterns in hyperdiverse, yet poorly understood regions like the Amazon Basin.

Medicinal Bioprospecting of the Amazon Rainforest: A Modern Eldorado?

Ignorant of the New World, Europeans believed in El Dorado, a hidden city of immense wealth in gold. Many consider the Amazonian forest to be a medicinal treasure chest and potentially the largest drug dispensary in the world. Yet, the quest to obtain drugs from indigenous tropical plants remains elusive. Here, we assess the potential of new technologies to tap into the metabolic diversity of tropical plants. We also consider how regulations affect access to plant resources. We conclude that, although the road to this medicinal El Dorado may be long and arduous, many other smaller but still valuable finds are hidden along the way.

GA, Comiskey JA, Damasco G, Dávila N, García-Villacorta R, Diaz PRS, Vincentini A, Emilio T, Levis C, Schietti J, Souza P, Alonso A, Dallmeier F, Ferreira LV, Neill D, Araujo-Murakami A, Arroyo L, Carvalho FA, Souza FC, do Amaral DD, Gribel R, Luize BG, Pansonato MP, Venticinque E, Fine P, Toledo M, Baraloto C, Cerón C, Engel J, Henkel TW, Jimenez EM, Maas P, Mora MCP, Petronelli P, Revilla JDC, Silveira M, Stropp J, Thomas-Caesar R, Baker TR, Daly D, Paredes MR, da Silva NF, Fuentes A, Jørgensen PM, Schöngart J, Silman MR, Arboleda NC, Cintra BBL, Valverde FC, Di Fiore A, Phillips JF, van Andel TR, von Hildebrand P, Barbosa EM, de Matos Bonates LC, de Castro D, de Sousa Farias E, Gonzales T, Guillaumet JL, Hoffman B, Malhi Y, de Andrade Miranda IP, Prieto A, Rudas A, Ruschell AR, Silva N, Vela CIA, Vos VA, Zent EL, Zent S, Cano A, Nascimento MT, Oliveira AA, Ramirez-Angulo H, Ramos JF, Sierra R, Tirado M, Medina MNU, van der Heijden G, Torre EV, Vriesendorp C, Wang O, Young KR, Baider C, Balslev H, de Castro N, Farfan-Rios W, Ferreira C, Mendoza C, Mesones I, Torres-Lezama A, Giraldo LEU, Villarroel D, Zagt R, Alexiades MN, Garcia-Cabrera K, Hernandez L, Huamantupa-Chuquimaco I, Milliken W, Cuenca WP, Pansini S, Pauletto D, Arevalo FR, Sampaio AF, Valderrama Sandoval EH, Gamarra LV. 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.

Regional Red List assessment of tree species in upper montane forests of the Tropical Andes

The Tropical Andes are characterized by a high level of endemism and plant species richness but are under pressure from human activities. We present the first regional conservation assessment of upper montane tree species in this region. We identified 3,750 tree species as occurring in this region, of which 917 were excluded because of a lack of data on their distribution. We identified a subset of 129 taxa that were restricted to higher elevations (> 1,500 m) but occurred in more than one country, thus excluding local endemics evaluated in previous national assessments. Distribution maps were created for each of these selected species, and extinction risk was assessed according to the IUCN Red List categories and criteria (version 3.1), drawing on expert knowledge elicited from a regional network of specialists. We assessed one species, Polylepis microphylla, as Critically Endangered, 47 species as Endangered and 28 as Vulnerable. Overall, 60% of the species evaluated were categorized as threatened, or 73% if national endemics are included. It is recommended that extinction risk assessments for tree species be used to inform the development of conservation strategies in the region, to avoid further loss of this important element of biodiversity.

Towards a Global Tree Assessment

Although trees have high economic, cultural and ecological value, increasing numbers of species are potentially at risk of extinction because of forest loss and degradation as a result of human activities, including overharvesting, fire and grazing. Emerging threats include climate change and its interaction with the spread of pests and diseases. The impact of such threats on the conservation status of trees is poorly understood. Here we highlight the need to conduct a comprehensive conservation assessment of the world's tree species, building on previous assessments undertaken for the IUCN Red List. We suggest that recent developments in plant systematics, online databases, remote sensing data and associated analytical tools offer an unprecedented opportunity to conduct such an assessment. We provide an overview of how a Global Tree Assessment could be achieved in practice, through participative, open-access approaches to data sharing and evaluation.

Are we filling the data void? An assessment of the amount and extent of plant collection records and census data available for tropical South America

Large-scale studies are needed to increase our understanding of how large-scale conservation threats, such as climate change and deforestation, are impacting diverse tropical ecosystems. These types of studies rely fundamentally on access to extensive and representative datasets (i.e., "big data"). In this study, I asses the availability of plant species occurrence records through the Global Biodiversity Information Facility (GBIF) and the distribution of networked vegetation census plots in tropical South America. I analyze how the amount of available data has changed through time and the consequent changes in taxonomic, spatial, habitat, and climatic representativeness. I show that there are large and growing amounts of data available for tropical South America. Specifically, there are almost 2,000,000 unique geo-referenced collection records representing more than 50,000 species of plants in tropical South America and over 1,500 census plots. However, there is still a gaping "data void" such that many species and many habitats remain so poorly represented in either of the databases as to be functionally invisible for most studies. It is important that we support efforts to increase the availability of data, and the representativeness of these data, so that we can better predict and mitigate the impacts of anthropogenic disturbances.

Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.

The transparency, reliability and utility of tropical rainforest land-use and land-cover change models

Land-use and land-cover (LULC) change is one of the largest drivers of biodiversity loss and carbon emissions globally. We use the tropical rainforests of the Amazon, the Congo basin and South-East Asia as a case study to investigate spatial predictive models of LULC change. Current predictions differ in their modelling approaches, are highly variable and often poorly validated. We carried out a quantitative review of 48 modelling methodologies, considering model spatio-temporal scales, inputs, calibration and validation methods. In addition, we requested model outputs from each of the models reviewed and carried out a quantitative assessment of model performance for tropical LULC predictions in the Brazilian Amazon. We highlight existing shortfalls in the discipline and uncover three key points that need addressing to improve the transparency, reliability and utility of tropical LULC change models: (1) a lack of openness with regard to describing and making available the model inputs and model code; (2) the difficulties of conducting appropriate model validations; and (3) the difficulty that users of tropical LULC models face in obtaining the model predictions to help inform their own analyses and policy decisions. We further draw comparisons between tropical LULC change models in the tropics and the modelling approaches and paradigms in other disciplines, and suggest that recent changes in the climate change and species distribution modelling communities may provide a pathway that tropical LULC change modellers may emulate to further improve the discipline. Climate change models have exerted considerable influence over public perceptions of climate change and now impact policy decisions at all political levels. We suggest that tropical LULC change models have an equally high potential to influence public opinion and impact the development of land-use policies based on plausible future scenarios, but, to do that reliably may require further improvements in the discipline.

Distribution and Conservation ofDavilla(Dilleniaceae) in Brazilian Atlantic Forest Using Ecological Niche Modeling

We have modeled the ecological niche for 12 plant species belonging to the genusDavilla(Dilleniaceae) which occur in the Atlantic Forest of Brazil. This group includes endemic species lianas threatened by extinction and is therefore a useful indicator for forest areas requiring conservation. The aims are to compare the distribution and richness of species within the protected areas, assessing the degree of protection and gap analysis of reserves for this group. We used the Maxent algorithm with environmental and occurrence data, and produced geographic distribution maps. The results show that high species richness occurs in forest and coastal forest of Espírito Santo to Bahia states. The endemic species compriseD. flexuosa, D. macrocarpa, D. flexuosa, D. grandifolia, andD. sessilifolia. In the Atlantic Forest of southeastern Brazil, the following endemic species occur:D. tintinnabulataandD. glaziovii, with this latter species being included in the “red list” due habitat loss and predatory extractivism. The indicators of species richness in the coastal region of Bahia correspond with floristic inventories that point to this area having a high biodiversity. Although this region has several protected areas, there are gaps in reserves, which, combined with anthropogenic threats and fragmentation, have caused several problems for biodiversity.

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.

Significance of endangered and threatened plant natural products in the control of human disease

One in five of the world's plant species is threatened with extinction according to the 2010 first global analysis of extinction risk. Tilman et al. predicted a massive ecological change to terrestrial plants within the next 50-100 y, accompanied by an increase in the number of global plant species facing extinction [Tilman D, et al. (2001) Proc Natl Acad Sci USA 98(10):5433-5440]. Most of the drug-producing plant families contain endangered species never previously studied for their utility to human health, which strongly validates the need to prioritize protection and assessment of these fragile and endangered groups [Zhu F, et al. (2011) Proc Natl Acad Sci USA 108(31):12943-12948]. With little prior attention given to endangered and rare plant species, this report provides strong justification for conservation of the rare plant Diplostephium rhododendroides Hieron., as well as other potential drug-producing endangered species in this and other groups.

Four decades of Andean timberline migration and implications for biodiversity loss with climate change

Rapid 21st-century climate change may lead to large population decreases and extinction in tropical montane cloud forest species in the Andes. While prior research has focused on species migrations per se, ecotones may respond to different environmental factors than species. Even if species can migrate in response to climate change, if ecotones do not they can function as hard barriers to species migrations, making ecotone migrations central to understanding species persistence under scenarios of climate change. We examined a 42-year span of aerial photographs and high resolution satellite imagery to calculate migration rates of timberline–the grassland-forest ecotone–inside and outside of protected areas in the high Peruvian Andes. We found that timberline in protected areas was more likely to migrate upward in elevation than in areas with frequent cattle grazing and fire. However, rates in both protected (0.24 m yr⁻¹) and unprotected (0.05 m yr⁻¹) areas are only 0.5–2.3% of the rates needed to stay in equilibrium with projected climate by 2100. These ecotone migration rates are 12.5 to 110 times slower than the observed species migration rates within the same forest, suggesting a barrier to migration for mid- and high-elevation species. We anticipate that the ecotone will be a hard barrier to migration under future climate change, leading to drastic population and biodiversity losses in the region unless intensive management steps are taken.

Tropical rain forest conservation and the twin challenges of diversity and rarity

Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.

The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes

Soil from the Amazonian region is usually regarded as unsuitable for agriculture because of its low organic matter content and low pH; however, this region also contains extremely rich soil, the Terra Preta Anthrosol. A diverse archaeal community usually inhabits acidic soils, such as those found in the Amazon. Therefore, we hypothesized that this community should be sensitive to changes in the environment. Here, the archaeal community composition of Terra Preta and adjacent soil was examined in four different sites in the Brazilian Amazon under different anthropic activities. The canonical correspondence analysis of terminal restriction fragment length polymorphisms has shown that the archaeal community structure was mostly influenced by soil attributes that differentiate the Terra Preta from the adjacent soil (i.e., pH, sulfur, and organic matter). Archaeal 16S rRNA gene clone libraries indicated that the two most abundant genera in both soils were Candidatus nitrosphaera and Canditatus nitrosocaldus. An ammonia monoxygenase gene (amoA) clone library analysis indicated that, within each site, there was no significant difference between the clone libraries of Terra Preta and adjacent soils. However, these clone libraries indicated there were significant differences between sites. Quantitative PCR has shown that Terra Preta soils subjected to agriculture displayed a higher number of amoA gene copy numbers than in adjacent soils. On the other hand, soils that were not subjected to agriculture did not display significant differences on amoA gene copy numbers between Terra Preta and adjacent soils. Taken together, our findings indicate that the overall archaeal community structure in these Amazonian soils is determined by the soil type and the current land use.