Biodiversity loss along a gradient of deforestation in Amazonian agricultural landscapes

The status of plant diversity in different land use types of agricultural landscape of west Oromia, Ethiopia

Understanding how land use types embedded in agricultural landscapes support forest biodiversity is critical, especially during this period of continuing fragmentation and habitat losses in natural ecosystems. Here, we explored the floristic species composition with respect to land use types in the agroecosystem of west Oromia, Ethiopia. For this, a systematic sampling method was employed to collect floristic data from 122 main quadrats and 610 sub-quadrats, following transects laid out with a 1500-m interval. The main quadrats were arranged on transects with an 800-m interval to assess woody species, and five sub-quadrats (i.e., four at the corners and one at the center) were taken within each main plot to assess herbaceous plants. Accordingly, the floristics were assessed with respect to the identified five land use types, including crop land, forest, grazing land, home gardens, and riverine. We used a one-way ANOVA to test the difference in species diversity among the land use types. Adonis 2 and indval functions were used to describe the species composition and indicator species in relation to the land use types. Moreover, NMDS was applied to visualize the associations of the species composition with environmental variables in ordination space. A total of 285 plant species belonging to 220 genera and 89 families were recorded. Our results showed significant differences in species diversity, dissimilarity in species composition, and species indicator values among the land use types. These results indicate that the potentiality of the land use types in supporting plant diversity is significantly different; for example, species diversity and abundances were higher in grazing lands and home gardens when compared with other land use types. Overall, our findings suggest that conservation strategies in agricultural landscapes should take into account the differences in capacity for supporting biodiversity among land use types when planning.

Caves as wildlife refuges in degraded landscapes in the Brazilian Amazon

Cross-habitat spillover may be the outcome of a process of habitat loss or degradation where the receiving habitat serves as a refuge for organisms. Once surface habitats are lost or degraded, animals can find underground refuge in caves. This paper is focused on testing whether taxonomic order richness inside caves is positively affected by the loss of the native vegetation cover surrounding caves; whether degradation of native vegetation cover predicts cave community composition; and whether there is a pattern of cave community clusters delimited by similarity in the effects of habitat degradation on animal communities. We gathered a comprehensive speleological dataset consisting of occurrence data of thousands of invertebrates and vertebrates sampled in 864 iron caves in the Amazon, to test the effects of both variables measured inside caves and surrounding landscapes on spatial variation in richness and composition of animal communities. We show that caves can work as refuges for the fauna in landscapes where the native vegetation cover surrounding them was degraded, which was evidenced by landcover change increasing the richness of cave communities and clustering caves by similarity in community composition. Therefore, habitat degradation on the surface should be a key variable when characterizing cave ecosystems for conservation prioritization and offset planning. Habitat degradation causing a cross-habitat spillover effect highlights the importance of maintaining the connection between caves by the surface, especially large caves. Our study can help guide industry and stakeholders working on the complex conciliation between land use and biodiversity conservation.

Molecular survey of Zika virus in the animal-human interface in traditional farming

Backyard animal husbandry is common in rural communities in developing countries and, given the conditions in which it occurs, it can increase the risk of disease transmission, such as arboviruses. To determine the presence of the Zika virus (ZIKV) and abundance of its arthropod vectors we evaluated the socioeconomic implications involved in its transmission in two highly vulnerable Mayan communities in the state of Yucatan that practice backyard farming. An analytical cross-sectional study was carried out throughout 2016 to understand socioeconomic variables and seasonal patterns in mosquito populations. We selected 20 households from each community. Social exclusion indicators were analyzed, human and domestic animals were sampled, and mosquitoes were collected and identified. Four out of eight indicators of social exclusion were higher than the reported national averages. We captured 5,825 mosquitoes from 16 species being Culex quinquefasciatus and Aedes aegypti the most abundant. The presence of chickens and human overcrowding in dwellings were the most significant factors (P = 0.026) associated with the presence of Ae. aegypti. Septic tanks (odds ratio = 6.64) and chickens (odds ratio = 27.41) in backyards were the main risk factors associated with the presence of immature states of Ae. aegypti in both communities. Molecular analysis to detect ZIKV was performed in blood samples from 416 humans, 1,068 backyard animals and 381 mosquito pools. Eighteen humans and 10 pig pools tested positive for ZIKV. Forty-three mosquito pools tested positive for flavivirus. Ten of the 43 pools of positive mosquitoes were sequenced, corresponding 3/10 to ZIKV and 1/10 to Dengue virus type 2. The findings obtained indicate the continuous circulation of Flavivirus (including ZIKV) in backyard environments in vulnerable communities, highlighting the importance of studying their transmission and maintenance in these systems, due that backyard animal husbandry is a common practice in these vulnerable communities with limited access to health services.

Changes in Cultivated Land Loss and Landscape Fragmentation in China from 2000 to 2020

Cultivated land area and fragmentation are two crucial elements that influence food production in China. However, few studies have analyzed the fine-grained changes in both the area and the fragmentation of cultivated land from a national perspective. Using a 30 m annual land-cover dataset with the help of cultivated land area (CA) and a newly constructed coupling landscape fragmentation index (CLFI), this research identified the spatial distribution characteristics of both the area and the landscape fragmentation of cultivated land in Chinese counties and simultaneously analyzed the changes in the above two elements since the beginning of the 21st century. The results showed that the distribution pattern of CA in China’s counties was large in the north and small in the south. During the first two decades of the 21st century, the total CA of China decreased, but the decrease rate decreased from 2.91% in 2000–2010 to 0.41% in 2010–2020; in contrast, the CLFI of China showed an increasing trend, but the increase rate also decreased, from 4.06% in 2000–2010 to 0.51% in 2010–2020. Spatially, from 2000 to 2010, there was an obvious reverse distribution pattern between counties with large CA changes and those with large CLFI changes; however, this pattern became less obvious from 2010 to 2020. Urban expansion, sloping land conversion programs and other ecological protection programs, and land development and consolidation programs were major causes of changes in the CA and CLFI across China. The findings of this research provide a data basis and scientific support for the protection and large-scale utilization of cultivated land, where this information is necessary to ensure food security.

Orchidaceae of the municipality of Igarapé-Miri, Pará, Brazilian Amazon

Abstract The municipality of Igarapé-Miri is located in the Endemism Center of Belém, which corresponds to the most deforested portion of the Brazilian Amazon with only 38% of its native forest remaining. The family Orchidaceae has several endemic taxa and expressive diversity in the Amazon phytogeographic domain, including in the state of Pará where 97 genera and 395 species have been reported. Considering the advanced state of fragmentation and the loss of diversity in the region, together with the lack of information about the flora of the municipality of Igarapé-Miri (Pará, Brazil), a floristic-taxonomic study was undertaken of the species of Orchidaceae in the municipality, including an identification key, morphological descriptions, taxonomic comments, illustrations and information on habitat, phenology and the geographic distribution of species. Fifty-eight species distributed in 38 genera were recorded for the municipality of Igarapé-Miri. The most diverse genera were Epidendrum (7 spp.) and Catasetum (4 spp.), followed by Maxillaria, Scaphyglottis and Stelis (3 spp. each). Most species occur as epiphytes and in Terra Firme Forest, with 31 species being exclusive to this type of vegetation. The occurrence of Anathallis fastigiata, Catasetum albovirens, Dichaea brachyphylla and Palmorchis triquilhada, species restricted to the Brazilian Amazon, stands out. The distribution of Stelis palmeiraensis is expanded to the Amazon phytogeographic domain and Stelis ciliaris and Uleiorchis ulei are documented in the state of Pará for the first time.

A "Dirty" Footprint: Macroinvertebrate diversity in Amazonian Anthropic Soils

Amazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems. We found 673 morphospecies and, despite similar richness in ADEs (385 spp.) and reference soils (399 spp.), we identified a tenacious pre-Columbian footprint, with 49% of morphospecies found exclusively in ADEs. Termite and total macroinvertebrate abundance were higher in reference soils, while soil fertility and macroinvertebrate activity were higher in the ADEs, and associated with larger earthworm quantities and biomass. We show that ADE habitats have a unique pool of species, but that modern land use of ADEs decreases their populations, diversity, and contributions to soil functioning. These findings support the idea that humans created and sustained high-fertility ecosystems that persist today, altering biodiversity patterns in Amazonia.

Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning

Background

The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited.

Methods

Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron.

Results

The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5-10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.

Epidemiology, Biodiversity, and Technological Trajectories in the Brazilian Amazon: From Malaria to COVID-19

The Amazon biome is under severe threat due to increasing deforestation rates and loss of biodiversity and ecosystem services while sustaining a high burden of neglected tropical diseases. Approximately two thirds of this biome are located within Brazilian territory. There, socio-economic and environmental landscape transformations are linked to the regional agrarian economy dynamics, which has developed into six techno-productive trajectories (TTs). These TTs are the product of the historical interaction between Peasant and Farmer and Rancher practices, technologies and rationalities. This article investigates the distribution of the dominant Brazilian Amazon TTs and their association with environmental degradation and vulnerability to neglected tropical diseases. The goal is to provide a framework for the joint debate of the local economic, environmental and health dimensions. We calculated the dominant TT for each municipality in 2017. Peasant trajectories (TT1, TT2, and TT3) are dominant in ca. fifty percent of the Amazon territory, mostly concentrated in areas covered by continuous forest where malaria is an important morbidity and mortality cause. Cattle raising trajectories are associated with higher deforestation rates. Meanwhile, Farmer and Rancher economies are becoming dominant trajectories, comprising large scale cattle and grain production. These trajectories are associated with rapid biodiversity loss and a high prevalence of neglected tropical diseases, such as leishmaniasis, Aedes-borne diseases and Chagas disease. Overall, these results defy simplistic views that the dominant development trajectory for the Amazon will optimize economic, health and environmental indicators. This approach lays the groundwork for a more integrated narrative consistent with the economic history of the Brazilian Amazon.

Seed Removal Rates in Forest Remnants Respond to Forest Loss at the Landscape Scale

Seed removal is a key component of seed dispersal and may be influenced by both landscape-scale and local attributes, and it has been used as an indicator of the intensity of interactions between ecosystem components. We examined how the seed removal rates, which integrate the activity of seed dispersers and seed predators, vary with landscape-scale forest cover. We collected data under 34 trees belonging to two zoochoric species (Helicostylis tomentosa (Poepp. and Endl.) J. F. Macbr. and Inga vera Willd.) in 17 remnants in the Brazilian Atlantic forest, with different percentages of forest cover. The seed removal rate was estimated using a fast method based on the abundance of intact fruits and fruit scraps on the ground. The amount of forest cover affected the rate of seed removal in a humpbacked shape, with a maximum seed removal rate at intermediate forest cover. Seed removal rates must be related to the amount of food resources offered and diversity of dispersers and predators in the region. In landscapes with intermediate forest amount, there is a better balance between supply and demand for fruits, leading to a higher seed removal rate than more deforested or forested landscape. Our results also show that local factors, such as crop size and canopy surface, together with forest cover amount, are also important to the removal rate, depending on the species. In addition, our results showed that plant–animal interactions are occurring in all fragments, but the health status of these forests is similar to disturbed forests, even in sites immersed in forested landscapes.

Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

Coordinated community structure among trees, fungi and invertebrate groups in Amazonian rainforests

Little is known regarding how trophic interactions shape community assembly in tropical forests. Here we assess multi-taxonomic community assembly rules using a rare standardized coordinated inventory comprising exhaustive surveys of five highly-diverse taxonomic groups exerting key ecological functions: trees, fungi, earthworms, ants and spiders. We sampled 36 1.9-ha plots from four remote locations in French Guiana including precise soil measurements, and we tested whether species turnover was coordinated among groups across geographic and edaphic gradients. All species group pairs exhibited significant compositional associations that were independent from soil conditions. For some of the pairs, associations were also partly explained by soil properties, especially soil phosphorus availability. Our study provides evidence for coordinated turnover among taxonomic groups beyond simple relationships with environmental factors, thereby refining our understanding regarding the nature of interactions occurring among these ecologically important groups.

Land Use Change in Coastal Cities during the Rapid Urbanization Period from 1990 to 2016: A Case Study in Ningbo City, China

Coastal cities have been experiencing tremendous land use changes worldwide. Studies on the consequences of land use change in coastal cities have provided helpful information for spatial regulations and have attracted increased attention. Changes in forests and water bodies, however, have rarely been investigated, challenging the formation of a holistic pattern of land use change. In this study, we selected Ningbo, China, as a case study area and analyzed its land use change from 1990 to 2016. Random forest (RF) classification was employed to derive land use information from Landsat images. Transition matrices and a distribution index (DI) were applied to identify the major types of land use transitions and their spatial variations by site-specific attributes. The results showed that the entire time period could be divided into two stages, based on the manifestations of land use change in Ningbo: 1990–2005 and 2005–2016. During 1990–2005, construction land expanded rapidly, mainly through the occupation of agricultural land and forest, while during 2005–2016, the main change trajectory turned out to be a small net change in construction land and a net increase in agricultural land sourced from construction land, forests, and water bodies. In terms of land use change by site-specific attributes, the rapid expansion of construction land around the municipal city center during 1990–2005 was restrained, and similar amounts of land conversion between construction and agricultural use occurred during 2005–2016. During the study period, areas undergoing land use change also showed trends of moving outward from the municipal city center and the county centers located adjacent to roads and the coastline and of moving up to hilly areas with steeper slopes and higher elevations. Protecting reclaimed agricultural land, improving the efficiency of construction land, and controlling forest conversion in hilly areas are suggested as spatial regulations in Ningbo city.

Anti-cancer drugs in aquatic environment can cause cancer: Insight about mutagenicity in tadpoles

Cyclophosphamide (Cyc) and 5-fluorouracil (5-FU) are two of the most used antineoplastic drugs (AD) in the world. However, their discharge in the environment became a yet-unknown environmental issue that has impact on some groups of animals, such as amphibians. We assessed tadpoles (Lithobates catesbeianus) exposed to environmental concentrations (EC) of Cyc and 5-FU to evaluate whether they can cause morphological and mutagenic changes in them. We defined the following groups: control, positive control (50 mg/L of Cyc), EC-Cyc-I (0.2 μg/L), EC-Cyc-II (0.5 μg/L), EF-Cyc (2.0 μg/L), EC-5-FU-I (13.0 μg/L), EC-5-FU-II (30.4 μg/L) and EF-5-FU (123.5 μg/L). EC groups presented predictive AD concentrations in 10% and 25% hospital-effluent dilutions in water. EF groups met gross hospital-effluent concentrations. Based on our data, ADs caused intestinal changes and influenced the interocular distance in tadpoles after 30-day exposure. We also observed the aneugenic and clastogenic effect of ADs due to the higher frequency of micronucleated and binucleated erythrocytes, and blebbed, multilobulated, notched and kidney-shaped nuclei in animals exposed to them. Based on such changes, we assume that Cyc and 5-FU can trigger malignant cell transformation processes, and cancer, in animals exposed to them, even at low concentrations. Our study is the first to describe that Cyc and 5-FU, spread in the environment, cause damages in non-target organisms opposite to their original end.