Biotic Research

Diversity of Metal-Resistant and Tensoactive-Producing Culturable Heterotrophic Bacteria Isolated from a Copper Mine in Brazilian Amazonia.

Bacterial extracellular polymeric substances (EPSs) present diverse properties of biotechnological interest, such as surface modification, metal adsorption and hydrophobic substances solubilization through surface tension reduction. Thus, there is a growing demand for new producing strains and structurally variable biomolecules with different properties. One approach for scanning this biodiversity consists of exploring environments under selective pressures. The aim of this study was to evaluate the composition of culturable heterotrophic bacterial communities from five different sites from a copper mine in the Amazon biome by an enrichment technique to obtain metal resistant bacteria (lead, arsenic, cadmium, copper and zinc) capable of producing EPSs. The bacterial densities at the sites varied from 2.42 × 103 to 1.34 × 108 NMP mL-1 and the 77 bacterial isolates obtained were classified in four divisions, β-Proteobacteria (16.88%), γ-Proteobacteria (7.29%), Firmicutes (61%) and Actinobacteria (12.98%). Bacillus, Alcaligenes, and Lysinibacillus were the most dominant among the 16 observed genera, but the relative frequency of each varied according to the sample and the metal used in the enrichment culture. 58% of the bacterial strains (45) could produce EPSs. From these, 33 strains showed emulsifying activity (E24), and 9 of them reached values higher than 49%. Only Actinomyces viscosus E3.Pb5 and Bacillus subtilis group E3.As2 reduced the medium surface tension to values lower than 35 mN m-1. It was possible to confirm the high presence of bacteria capable of producing EPSs with tensoactive properties in Amazon copper mines and the evolutionary pressure exerted by the heavy metals during enrichment. These molecules can be tested as an alternative for use in processes that involve the removal of metals, such as the bioremediation of contaminated environments.

Mitigation strategies to reverse the rising trend of plastics in Polar Regions.

Plastic marine pollution in the Arctic today illustrates the global distribution of plastic waste of all sizes traveling by wind and waves, entering food chains, and presenting challenges to management and mitigation. While currents move plastics from lower latitudes into the Arctic, significant waste is also generated by remote communities, as well as maritime activities, such as shipping, fishing and tourism, which are increasing their activities as seasonal sea ice diminishes. Mitigation strategies may include monitoring programs of plastic waste abundance and distribution, improved waste management in Arctic communities, Extended Producer Responsibility (EPR) to reverse the transport of waste plastics and packaging from remote communities, incentivized gear recovery of abandoned, lost and discarded fishing gear (ALDFG), gear tagging and tracking, and restricting tourism and employing “leave no trace” policies. Here we report how these mitigation strategies are employed in the Arctic to minimize plastic waste impacts, and move Arctic communities toward better materials management and circular economic practices. The evidence of harm from waste plastics exacerbated by the ubiquity of plastic marine pollution in all biomes, and the rapid reporting of ecological and social costs, together suggest that we know enough to act quickly to manage and mitigate plastics from all sources to the Arctic.

Spatial and temporal structure of diversity and demographic dynamics along a successional gradient of tropical forests in southern Brazil.

Analysis of the structure, diversity, and demographic dynamics of tree assemblages in tropical forests is especially important in order to evaluate local and regional successional trajectories.We conducted a long-term study to investigate how the structure, species richness, and diversity of secondary tropical forests change over time. Trees (DBH ≥ 5 cm) in the Atlantic Forest of southern Brazil were sampled twice during a 10-year period (2007 and 2017) in six stands (1 ha each) that varied in age from their last disturbance (25, 60, 75, 90, and more than 100 years). We compared forest structure (abundance and basal area), species richness, alpha diversity, demographic rates (mortality, recruitment, and loss or gain in basal area), species composition, spatial beta diversity, and temporal beta diversity (based on turnover and nestedness indices) among stand ages and study years.Demographic rates recorded in a 10-year interval indicate a rapid and dynamic process of species substitution and structural changes. Structural recovery occurred faster than beta diversity and species composition recovery. The successional gradient showed a pattern of species trade-off over time, with less spatial dissimilarity and faster demographic rates in younger stands. As stands grow older, they show larger spatial turnover of species than younger stands, making them more stochastic in relation to species composition. Stands appear to split chronologically to some extent, but not across a straightforward linear axis, reflecting stochastic changes, providing evidence for the formation of a nonequilibrium community. Policy implications. These results reiterate the complexity and variability in forest succession and serve as a reference for the evaluation and monitoring of local management and conservation actions and for defining regional strategies that consider the diversity of local successional trajectories to evaluate the effectiveness of restoration measures in secondary forests of the Atlantic Forest biome.

Carboniferous plant physiology breaks the mold.

How plants have shaped Earth surface feedbacks over geologic time is a key question in botanical and geological inquiry. Recent work has suggested that biomes during the Carboniferous Period contained plants with extraordinary physiological capacity to shape their environment, contradicting the previously dominant view that plants only began to actively moderate the Earth’s surface with the rise of angiosperms during the Mesozoic Era. A recently published Viewpoint disputes this recent work, thus here, we document in detail, the mechanistic underpinnings of our modeling and illustrate the extraordinary ecophysiological nature of Carboniferous plants.

Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum.

Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, while incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize in our ongoing worldwide monographic treatment of the group. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, while the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. It will be critical to take advantage of all available lines of evidence to decipher events in the distant past. The joint estimation approach developed here provides cautious hope even when fossil evidence is limited.

The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials.

The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in Colombian Paramos using 16S rRNA gene amplicon sequencing and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes varied in diversity indexes and number of OTUs, but were composed predominantly by the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia. In the case of Cora and Cladonia, the microbiomes were distinguished based on the identity of the lichen host. While the majority of the lichen-associated microorganisms were not present in all lichens sampled, sixteen taxa shared among this diverse group of lichens suggest a core lichen microbiome that broadens our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant microbial strains. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.

An operational definition of the biome for global change research.

Biomes are constructs for organising knowledge on the structure and functioning of the world’s ecosystems, and serve as useful units for monitoring how the biosphere responds to anthropogenic drivers, including climate change. The current practice of delimiting biomes relies on expert knowledge. Recent studies have questioned the value of such biome maps for comparative ecology and global-change research, partly due to their subjective origin. Here we propose a flexible method for developing biome maps objectively. The method uses range modelling of several thousands of plant species to reveal spatial attractors for different growth-form assemblages that define biomes. The workflow is illustrated using distribution data from 23,500 African plant species. In an example application, we create a biome map for Africa and use the fitted species models to project biome shifts. In a second example, we map gradients of growth-form suitability that can be used to identify sites for comparative ecology. This method provides a flexible framework that allows a range of biome types to be defined according to user needs. The method also enables projections of biome changes that emerge purely from the individualistic responses of plant species to environmental changes.

Faster Atlantic currents drive poleward expansion of temperate phytoplankton in the Arctic Ocean.

The Arctic marine biome, shrinking with increasing temperature and receding sea-ice cover, is tightly connected to lower latitudes through the North Atlantic. By flowing northward through the European Arctic Corridor (the main Arctic gateway where 80% of in- and outflow takes place), the North Atlantic Waters transport most of the ocean heat, but also nutrients and planktonic organisms toward the Arctic Ocean. Using satellite-derived altimetry observations, we reveal an increase, up to two-fold, in North Atlantic current surface velocities over the last 24 years. More importantly, we show evidence that the North Atlantic current and its variability shape the spatial distribution of the coccolithophore Emiliania huxleyi (Ehux), a tracer for temperate ecosystems. We further demonstrate that bio-advection, rather than water temperature as previously assumed, is a major mechanism responsible for the recent poleward intrusions of southern species like Ehux. Our findings confirm the biological and physical “Atlantification” of the Arctic Ocean with potential alterations of the Arctic marine food web and biogeochemical cycles.

Integrating multiple sources of ecological data to unveil macroscale species abundance.

The pattern of species abundance, represented by the number of individuals per species within an ecological community, is one of the fundamental characteristics of biodiversity. However, despite their obvious significance in ecology and biogeography, there is still no clear understanding of these patterns at large spatial scales. Here, we develop a hierarchical modelling approach to estimate macroscale patterns of species abundance. Using this approach, estimates of absolute abundance of 1248 woody plant species at a 10-km-grid-square resolution over East Asian islands across subtropical to temperate biomes are obtained. We provide two examples of the basic and applied use of the estimated species abundance for (1) inference of macroevolutionary processes underpinning regional biodiversity patterns and (2) quantitative community-wide assessment of a national red list. These results highlight the potential of the elucidation of macroscale species abundance that has thus far been an inaccessible but critical property of biodiversity.

Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient.

Global biodiversity currently peaks at the equator and decreases toward the poles. Growing fossil evidence suggest this hump-shaped latitudinal diversity gradient (LDG) has not been persistent through time, with similar diversity across latitudes flattening out the LDG during past greenhouse periods. However, when and how diversity declined at high latitudes to generate the modern LDG remains an open question. Although diversity-loss scenarios have been proposed, they remain mostly undemonstrated. We outline the ‘asymmetric gradient of extinction and dispersal’ framework that contextualizes previous ideas behind the LDG under a time-variable scenario. Using phylogenies and fossils of Testudines, Crocodilia and Lepidosauria, we find that the hump-shaped LDG could be explained by (1) disproportionate extinctions of high-latitude tropical-adapted clades when climate transitioned from greenhouse to icehouse, and (2) equator-ward biotic dispersals tracking their climatic preferences when tropical biomes became restricted to the equator. Conversely, equivalent diversification rates across latitudes can account for the formation of an ancient flat LDG. The inclusion of fossils in macroevolutionary studies allows revealing time-dependent extinction rates hardly detectable from phylogenies only. This study underscores that the prevailing evolutionary processes generating the LDG during greenhouses differed from those operating during icehouses. This article is protected by copyright. All rights reserved.

Competition influences tree growth, but not mortality, across environmental gradients in Amazonia and tropical Africa.

Competition among trees is an important driver of community structure and dynamics in tropical forests. Neighboring trees may impact an individual tree’s growth rate and probability of mortality, but large-scale geographic and environmental variation in these competitive effects has yet to be evaluated across the tropical forest biome. We quantified effects of competition on tree-level basal area growth and mortality for trees ≥ 10 cm diameter across 151 ~1-ha plots in mature tropical forests in Amazonia and tropical Africa by developing non-linear models that accounted for wood density, tree size and neighborhood crowding. Using these models, we assessed how water availability (i.e., climatic water deficit) and soil fertility influenced the predicted plot-level strength of competition (i.e., the extent to which growth is reduced, or mortality is increased, by competition across all individual trees). On both continents, tree basal area growth decreased with wood density, and increased with tree size. Growth decreased with neighborhood crowding, which suggests that competition is important. Tree mortality decreased with wood density and generally increased with tree size, but was apparently unaffected by neighborhood crowding. Across plots, variation in the plot-level strength of competition was most strongly related to plot basal area (i.e., the sum of the basal area of all trees in a plot), with greater reductions in growth occurring in forests with high basal area, but in Amazonia the strength of competition also varied with plot-level wood density. In Amazonia, the strength of competition increased with water availability because of the greater basal area of wetter forests, but was only weakly related to soil fertility. In Africa, competition was weakly related to soil fertility, and invariant across the shorter water availability gradient. Overall, our results suggest that competition influences the structure and dynamics of tropical forests primarily through effects on individual tree growth rather than mortality, and that the strength of competition largely depends on environment-mediated variation in basal area.

Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths.

Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed.

Playback point counts and N-mixture models suggest higher than expected abundance of the critically endangered blond titi monkey in northeastern Brazil.

Effective management of threatened species requires accurate population size estimation and monitoring. However, reliable population size estimates are lacking for many endangered species. The critically endangered blond titi monkey (Callicebus barbarabrownae) is an endemic primate of the Caatinga biome in Northeastern Brazil. A previous assessment based on presence-only data estimated a minimum population size of 260 mature individuals in 2,636 km2 , and studies based on visual records suggested very low local relative abundance. However, this cryptic species is known to be difficult to visually detect. We played back recordings of C. barbarabrownae loud calls to count the number of responding groups in 34 sampling sites during 9 consecutive days in a 221-km2 study area. Repeated group counts at sites were used in N-mixture models, which account for imperfect detection, to estimate the number of groups in relation to dry forest area and distance to villages. We estimated a total of 91 groups in the study area. Considering the mean number of adults per group as three, we estimated a population of 273 adult individuals, resulting in a density of 2.3 individuals/km2 in the dry forest habitat. Detection probability was four times higher for surveys conducted between sunrise to midmorning than between midmorning to sunset. We also found that C. barbarabrownae abundance increases with increasing dry forest area and increasing distance to the nearest village, indicating the need to promote dry forest restoration in the Caatinga. As our results suggest a larger population of C. barbarabrownae than had been previously estimated for its entire distribution, our results suggest a need for similar assessments in other areas to reliably estimate the total population size. This study demonstrates how playback surveys coupled with N-mixture models can be used to estimate population sizes of acoustically-responsive primates, and thus contribute to more effective conservation management.

Population structure of Fusarium graminearum isolated from different sources in one area over the course of three years.

Fusarium head blight (FHB) is an important crop disease worldwide and is mainly caused by members of the Fusarium graminearum species complex. F. graminearum sensu stricto is the most common cosmopolitan and predominant FHB causal agent in Europe. So far, the majority of studies have focused on the primary hosts (wheat and barley) of this pathogen, while the relationships between other sources of infection remain unclear. We monitored and sampled test fields over the course of three years and acquired 804 F. graminearum isolates from different sources: primary hosts and other plant species included in the crop rotations, weeds from the test fields, decaying plant residue, soil samples,

and crop seeds. Of these isolates, 73.3% had the 15-acetyldeoxynivalenol genotype and 26.7% had the 3-acetyldeoxynivalenol genotype. F. graminearum isolation rates from weeds (> 50%) were much higher than from soil (< 10%) or decaying plant matter (4%). Variable number of tandem repeat (VNTR) markers were used for population analysis. Noticeable genetic differentiation was detected between isolates from living plants and soil biome. In contrast, absence of any noticeable division between primary and alternative plant host communities, indicate the importance of weeds and other segetal plants for FHB control and prevention.

Tolerance evaluation and morphophysiological responses of Astronium graveolens, a native brazilian Cerrado, to addition of lead in soil.

Since the ecosystem is contaminated by lead, decontamination is a difficult and expensive process. Therefore, an alternative would be the use of phytoremediation plants, which have been studied more intensely in recent decades. Astronium graveolens Jacq (Anacardiaceae) is a Cerrado native species and plants of this biome are known to present adaptations and modifications that keep them in this ecosystem. Our aim was to find the tolerance index of A. graveolens to lead doses and to evaluate the morphophysiological alterations of the species when exposed to the heavy metal. The experiment was carried out in a greenhouse in Ilha Solteira-SP, with a completely randomized design and using lead acetate (Pb(C2H3O2)2) as the source of the heavy metal. Samples of the vegetative organs (roots and leaves) were fixed, subsequently dehydrated in an ethyl series, included in hydroxyethyl methacrylate (Leica Historesin) and sectioned for histological slide assembly and subsequent anatomical analysis. The levels of phenolic compounds, protein, amino acid, ammonia, allantoic acid and allantoin were quantified. We calculated the tolerance index for the species. Significant differences were found in leaf and root tissues anatomy, while in relation to the physiology of A. graveolens, a significant difference was observed when the concentration of total ureids in the roots was evaluated. Pb did not interfere with the survivability of the species. In fact, A. graveolens showed a higher secondary growth in the treatment with higher level of lead.

Species identity and diversity effects on invasion resistance of tropical freshwater plant communities.

Biotic resistance mediated by native plant diversity has long been hypothesized to reduce the success of invading plant species in terrestrial systems in temperate regions. However, still little is known about the mechanisms driving invasion patterns in other biomes or latitudes. We help to fill this gap by investigating how native plant community presence and diversity, and the presence of native phylogenetically closely related species to an invader, would affect invader Hydrilla verticillata establishment success in tropical freshwater submerged plant communities.