Significance of AI-assisted techniques for epiphyte plant monitoring and identification from drone images.

Monitoring forest canopies is vital for ecological studies, particularly for assessing epiphytes in rain forest ecosystems. Traditional methods for studying epiphytes, such as climbing trees and building observation structures, are labor, cost intensive and risky. Unmanned Aerial Vehicles (UAVs) have emerged as a valuable tool in this domain, offering botanists a safer and more cost-effective means to collect data. This study leverages AI-assisted techniques to enhance the identification and mapping of epiphytes using UAV imagery. The primary objective of this research is to evaluate the effectiveness of AI-assisted methods compared to traditional approaches in segmenting/identifying epiphytes from UAV images collected in a reserve forest in Costa Rica. Specifically, the study investigates whether Deep Learning (DL) models can accurately identify epiphytes during complex backgrounds, even with a limited dataset of varying image quality. Systematically, this study compares three traditional image segmentation methods Auto Cluster, Watershed, and Level Set with two DL-based segmentation networks: the UNet and the Vision Transformer-based TransUNet. Results obtained from this study indicate that traditional methods struggle with the complexity of vegetation backgrounds and variability in target characteristics. Epiphyte identification results were quantitatively evaluated using the Jaccard score. Among traditional methods, Watershed scored 0.10, Auto Cluster 0.13, and Level Set failed to identify the target. In contrast, AI-assisted models performed better, with UNet scoring 0.60 and TransUNet 0.65. These results highlight the potential of DL approaches to improve the accuracy and efficiency of epiphyte identification and mapping, advancing ecological research and conservation.

Nanoparticles and plants: A focus on analytical characterization techniques.

Nanotechnology has brought about significant progress through the use of goods based on nanomaterials. However, concerns remain about the accumulation of these materials in the environment and their potential toxicity to living organisms. Plants have the ability to take in nanomaterials (NMs), which can cause changes in their physiology and morphology. On the other hand, nanoparticles (NPs) have been used to increase plant development and control pests in agriculture by including them into agrochemicals. The challenges of the interaction, internalization, and accumulation of NMs within plant tissues are enormous, mainly because of the various characteristics of NMs and the absence of reliable analytical tools. As our knowledge of the interactions between NMs and plant cells expands, we are able to create novel NMs that are tailored, targeted, and designed to be safe, thus minimizing the environmental consequences of nanomaterials. This review provides a thorough examination and comparison of the main microscopy techniques, spectroscopic methods, and far-field super-resolution methodologies used to examine nanomaterials within the cell walls of plants.

Examining the interaction between pesticides and bioindicator plants: an in-depth analysis of their cytotoxicity.

Agrochemicals are substances used to prevent, destroy, or mitigate any pest. Their indiscriminate use can cause serious problems in ecosystems, contaminating surface and groundwater and affecting surrounding biota. However, in the environment, various natural processes such as biological degradation and photodegradation can mitigate their persistence and, consequently, their ecotoxicological impact. In this regard, this study aimed to obtain relevant data on the cytotoxic effects produced by pesticides on bioindicator plants. As observed in the literature review, cellular inhibition, nuclear anomalies, and micronucleus index are some of the different impacts commonly known from pesticides. These chemical substances can cause cytogenetic alterations in a plant bioassay. Plant bioindicators such as Allium cepa L, Vicia faba L, Pisum sativum L, Lactuca sativa L, and Lens culinaris Med are very important and effective experimental models for identifying the cytogenotoxicity of pesticides. These have been available for many years. However, they are still used today for their effectiveness in detecting and monitoring chemical substances such as agrochemicals.

Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants.

Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.

Time since fire as a driver of taxonomic and phylogenetic patterns of grassland plant communities.

Fire plays a key role in grasslands, determining the distribution and evolution of species and boundaries with neighboring ecosystems. Evidence of community-wide responses to fire is largely based on taxonomic and functional descriptors, while the phylogenetic dimension is overlooked. Here we evaluated how the taxonomic and phylogenetic structure of grassland plant communities responded to a time since fire (TSF) gradient. We sampled 12 communities in Southern Brazil under varying TSF and calculated taxonomic species richness (S) and dominance (D), phylogenetic diversity (PD), and mean phylogenetic distances (MPD). We used Structural Equation Models to test the relationships between the environmental gradient and community descriptors. Communities with longer TSF presented higher PD and MPD but lower species richness and increased taxonomic dominance. These sites were dominated by monocots, specifically C4 grasses, but also presented exclusive clades, whereas recently-burned sites presented lower taxonomic dominance and more species distributed in a wider variety of clades. Our results indicate that these scenarios are interchangeable and dependent on fire management. Fire adaptation was not constrained by phylogenetic relatedness, contrasting with previous findings for tropical savannahs and indicating that temperate and tropical non-forest ecosystems from South America respond differently to fire, possibly due to different evolutionary histories.

Agro-Industrial By-Products of Plant Origin: Therapeutic Uses as well as Antimicrobial and Antioxidant Activity.

The importance of bioactive compounds in agro-industrial by-products of plant origin lies in their direct impacts on human health. These compounds have been shown to possess antioxidant, anti-inflammatory, and antimicrobial properties, contributing to disease prevention and strengthening the immune system. In particular, the antimicrobial action of these compounds emerges as an important tool in food preservation, providing natural alternatives to synthetic preservatives and contributing to combating antimicrobial resistance. Using agro-industrial by-products of plant origin not only addresses the need to reduce waste and promote sustainability but also inaugurates a new era in the formulation of functional foods. From fruit peels to pulps and seeds, these by-products are emerging as essential ingredients in the creation of products that can promote health. Continued research in this area will unveil new applications and properties of these by-products and open doors to a food paradigm in which health and sustainability converge, paving the way to a healthier and more equitable future. The present review presents an overview of our knowledge of agro-industrial by-products and some of their more relevant health-promoting bioactivities.

Nature portrayed in images in Dutch Brazil: Tracing the sources of the plant woodcuts in the Historia Naturalis Brasiliae (1648).

By the mid-seventeenth century, images of natural elements that originated in Dutch Brazil circulated in Europe. These were often included in art collections (the Libri Picturati) and natural history treatises (the Historia Naturalis Brasiliae and the India Utriesque re Naturale et Medica, 1658). The plant woodcut images in these books constituted (icono) type specimens and played a significant role in disseminating scientific botanical knowledge. We present a systematic analysis of their origins by cross-referencing the visual and textual sources related to Dutch Brazil. To do so, we used our previous botanical identifications of the portrayed plants, published sources, and digital archival material. The plant woodcuts accounted for 529 images, which corresponded to 426 taxa. We created a PDF booklet to visualize the (dis-) similarities of the woodcuts with the Libri Picturati and other visual sources. Substantial differences in the visual-making methodology exist between the two treatises (1648, 1658). In the first book, most of the images were available from Dutch Brazil and carved into the woodcuts, while most of these woodcuts were reused in the second one. The Indigenous Tupi-based plant names accompanying the images were crucial when arranging the sources, and portraying as much botanical information as possible was commonly the goal. Freshly picked, living plants, dried branches, fruits, and seeds were used to represent the megadiverse Brazilian flora, even when these belonged to species originating from other regions. Despite not being recognized for their contribution, Indigenous Brazilians and enslaved Africans were essential in the visual knowledge-making processes that later resulted in these natural history collections. As several sources remain lost and many histories yet untold, further archival studies and collaborative projects are pertinent to reveal the missing pieces of this conundrum.

Use of Electron Microscopy for the Detection of Contaminant Endophytic Bacteria In Vitro.

The success of in vitro cultivation, particularly for micropropagation purposes, depends on the efficient control of contaminants. In this context, the sterilization of plant material constitutes a fundamental step in initiating cultures. Microbial contaminants can be found either on the surface (epiphyte) or inside plant explants (endophyte). However, the latter is generally challenging to detect and may not always be eradicated through surface sterilization alone. Endophyte contaminants, such as bacteria, can persist within plant material over several cultivation cycles, potentially interfering with or inhibiting in vitro establishment, growth, or recovery of cryopreserved materials. Therefore, microscopy techniques, such as electron microscopy, can yield valuable insights into bacterial endophytes' localization, tissue colonization patterns, and functions in in vitro plant culture. This information is essential for adopting effective strategies for eliminating, preventing, or harmonious coexistence with contaminants.

Plant Micropropagation and Temporary Immersion Systems.

Temporary immersion systems (TIS) have been widely recognized as a promising technology for micropropagation of various plant species. The TIS provides a suitable environment for culture and allows intermittent contact of the explant with the culture medium at different immersion frequencies and aeration of the culture in each cycle. The frequency or immersion is one of the most critical parameters for the efficiency of these systems. The design, media volume, and container capacity substantially improve cultivation efficiency. Different TIS have been developed and successfully applied to micropropagation in various in vitro systems, such as sprout proliferation, microcuttings, and somatic embryos. TIS increases multiplication and conversion rates to plants and a better response during the ex vitro acclimatization phase. This article covers the use of different immersion systems and their applications in plant biotechnology, particularly in plant tissue culture, as well as its use in the massive propagation of plants of agroeconomic interest.

A Novel Method for In Situ RT-PCR Based on Capsules from Centrifuge Tubes, Ideal for Transcripts Detection in Plant Tissues.

In situ RT-PCR presents advantages over other expression analysis methods due to its rapid processing and low-cost equipment. However, this technique is not without its challenges. A protocol based on a capsule made from centrifuge tubes that offers advantages over slides is presented. This capsule protects histological sections from drying out, and its easy assembly reduces time pauses between incubations. In addition, the container size where the sample is deposited allows the addition and withdrawal of the different solutions. The capsule does not need previous sealing after each incubation, and, above all, it is a low-cost and accessible material. A guideline for tissue sectioning using a cryostat that offers advantages over other sectioning methods is also described.

An Introduction to Plant Cell, Tissue, and Organ Culture: Current Status and Perspectives.

Plant cell, tissue, and organ cultures (PCTOC) have been used as experimental systems in basic research, allowing gene function demonstration through gene overexpression or repression and investigating the processes involved in embryogenesis and organogenesis or those related to the potential production of secondary metabolites, among others. On the other hand, PCTOC has also been applied at the commercial level for the vegetative multiplication (micropropagation) of diverse plant species, mainly ornamentals but also horticultural crops such as potato or fruit and tree species, and to produce high-quality disease-free plants. Moreover, PCTOC protocols are important auxiliary systems in crop breeding crops to generate pure lines (homozygous) to produce hybrids for the obtention of polyploid plants with higher yields or better performance. PCTOC has been utilized to preserve and conserve the germplasm of different crops or threatened species. Plant genetic improvement through genetic engineering and genome editing has been only possible thanks to the establishment of efficient in vitro plant regeneration protocols. Different companies currently focus on commercializing plant secondary metabolites with interesting biological activities using in vitro PCTOC. The impact of omics on PCTOC is discussed.

The History of Agrobacterium Rhizogenes: From Pathogen to a Multitasking Platform for Biotechnology.

Agrobacterium's journey has been a roller coaster, from being a pathogen to becoming a powerful biotechnological tool. While A. tumefaciens has provided the scientific community with a versatile tool for plant transformation, Agrobacterium rhizogenes has given researchers a Swiss army knife for developing many applications. These applications range from a methodology to regenerate plants, often recalcitrant, to establish bioremediation protocols to a valuable system to produce secondary metabolites. This chapter reviews its discovery, biology, controversies over its nomenclature, and some of the multiple applications developed using A. rhizogenes as a platform.

Plant development and reproduction in a changing environment.

Plants face the most diverse climatic conditions throughout their life cycle. As sessile organisms, they are remarkably resilient to adverse environments, which have been exacerbated in the current context of global change. The way in which plants sense and respond to various types of abiotic stresses varies depending on the severity of the stress and the developmental stage of the plant, affecting both vegetative and reproductive aspects. Understanding how plants respond and adapt to a changing environment is crucial for predicting and mitigating the impacts of climate change on ecosystems and ensuring the future survival and reproduction of plant species.

The Tropical Andes Biodiversity Hotspot: A Comprehensive Dataset for the Mira-Mataje Binational Basins.

We present a flora and fauna dataset for the Mira-Mataje binational basins. This is an area shared between southwestern Colombia and northwestern Ecuador, where both the Chocó and Tropical Andes biodiversity hotspots converge. We systematized data from 120 sources in the Darwin Core Archive (DwC-A) standard and geospatial vector data format for geographic information systems (GIS) (shapefiles). Sources included natural history museums, published literature, and citizen science repositories across 13 countries. The resulting database has 33,460 records from 6,821 species, of which 540 have been recorded as endemic, and 612 as threatened. The diversity represented in the dataset is equivalent to 10% of the total plant species and 26% of the total terrestrial vertebrate species in both hotspots. The dataset can be used to estimate and compare biodiversity patterns with environmental parameters and provide value to ecosystems, ecoregions, and protected areas. The dataset is a baseline for future assessments of biodiversity in the face of environmental degradation, climate change, and accelerated extinction processes.

Experimental evidence of climate change extinction risk in Neotropical montane epiphytes.

Climate change is conjectured to endanger tropical species, particularly in biodiverse montane regions, but accurate estimates of extinction risk are limited by a lack of empirical data demonstrating tropical species' sensitivity to climate. To fill this gap, studies could match high-quality distribution data with multi-year transplant experiments. Here, we conduct field surveys of epiphyte distributions on three mountains in Central America and perform reciprocal transplant experiments on one mountain across sites that varied in elevation, temperature and aridity. We find that most species are unable to survive outside of their narrow elevational distributions. Additionally, our findings suggest starkly different outcomes from temperature conditions expected by 2100 under different climate change scenarios. Under temperatures associated with low-emission scenarios, most tropical montane epiphyte species will survive, but under emission scenarios that are moderately high, 5-36% of our study species may go extinct and 10-55% of populations may be lost. Using a test of tropical species' climate tolerances from a large field experiment, paired with detailed species distribution data across multiple mountains, our work strengthens earlier conjecture about risks of wide-spread extinctions from climate change in tropical montane ecosystems.

The human touch: a meta-analysis of anthropogenic effects on plant-pollinator interaction networks.

Background: Anthropogenic activities significantly impact natural ecosystems, leading to alterations in plant and pollinator diversity and abundance. These changes often result in shifts within interacting communities, potentially reshaping the structure of plant-pollinator interaction networks. Given the escalating human footprint on habitats, evaluating the response of these networks to anthropization is critical for devising effective conservation and management strategies. Methods: We conducted a comprehensive review of the plant-pollinator network literature to assess the impact of anthropization on network structure. We assessed network metrics such as nestedness measure based on overlap and decreasing fills (NODF), network specialization (H2'), connectance (C), and modularity (Q) to understand structural changes. Employing a meta-analytical approach, we examined how anthropization activities, such as deforestation, urbanization, habitat fragmentation, agriculture, intentional fires and livestock farming, affect both plant and pollinator richness. Results: We generated a dataset for various metrics of network structure and 36 effect sizes for the meta-analysis, from 38 articles published between 2010 and 2023. Studies assessing the impact of agriculture and fragmentation were well-represented, comprising 68.4% of all studies, with networks involving interacting insects being the most studied taxa. Agriculture and fragmentation reduce nestedness and increase specialization in plant-pollinator networks, while modularity and connectance are mostly not affected. Although our meta-analysis suggests that anthropization decreases richness for both plants and pollinators, there was substantial heterogeneity in this regard among the evaluated studies. The meta-regression analyses helped us determine that the habitat fragment size where the studies were conducted was the primary variable contributing to such heterogeneity. Conclusions: The analysis of human impacts on plant-pollinator networks showed varied effects worldwide. Responses differed among network metrics, signaling nuanced impacts on structure. Activities like agriculture and fragmentation significantly changed ecosystems, reducing species richness in both pollinators and plants, highlighting network vulnerability. Regional differences stressed the need for tailored conservation. Despite insights, more research is crucial for a complete understanding of these ecological relationships.

Emerging roles of plant transcriptional gene silencing under heat.

Plants continuously endure unpredictable environmental fluctuations that upset their physiology, with stressful conditions negatively impacting yield and survival. As a contemporary threat of rapid progression, global warming has become one of the most menacing ecological challenges. Thus, understanding how plants integrate and respond to elevated temperatures is crucial for ensuring future crop productivity and furthering our knowledge of historical environmental acclimation and adaptation. While the canonical heat-shock response and thermomorphogenesis have been extensively studied, evidence increasingly highlights the critical role of regulatory epigenetic mechanisms. Among these, the involvement under heat of heterochromatic suppression mediated by transcriptional gene silencing (TGS) remains the least understood. TGS refers to a multilayered metabolic machinery largely responsible for the epigenetic silencing of invasive parasitic nucleic acids and the maintenance of parental imprints. Its molecular effectors include DNA methylation, histone variants and their post-translational modifications, and chromatin packing and remodeling. This work focuses on both established and emerging insights into the contribution of TGS to the physiology of plants under stressful high temperatures. We summarized potential roles of constitutive and facultative heterochromatin as well as the most impactful regulatory genes, highlighting events where the loss of epigenetic suppression has not yet been associated with corresponding changes in epigenetic marks.

Pollen analysis of honey and pollen stored by Melipona (Melikerria) fasciculata Smith, 1854 (Apidae Meliponini), in an Amazon and Cerrado transition area, Maranhão, Brazil.

The identification of meliponicultural flora is fundamental for the preservation of bees, as well as enabling the development of pollinator management and reforestation programs. In this context, this study aimed to investigate the types of pollen found in the honey and pollen pots of the Melipona fasciculata bee in Arari, State of Maranhão, between August 2022 and July 2023. 40 types of pollen were identified, distributed among 18 botanical families, with Fabaceae standing out (46.15% in pollen pots and 37.86% in honey pots), Myrtaceae (11.53% in pollen and 13.51% in honey) and Rubiaceae (7.69% in pollen and 5.40% in honey). Sapindaceae, in the honey pots, accounted for 5.40%. The other families showed lower percentages, 3.84% in the pollen pots and 2.70% in the honey pots. In terms of similarity, two distinct groups were observed in both the pollen and honey pots. In the pollen pots, group A (May-June ~ 97%) and group B (Feb-Mar ~ 99%) stood out, while in the honey pots, group A (Mar-Apr ~ 98%) and group B (Jun-Jul-Sept ~ 98%) showed the highest percentages. These findings highlight the wide range of resources used by the M. fasciculata species, as well asits preference for Fabaceae and Myrtaceae, due to the diversity and availability of trophic resources. An understanding of the meliponicultural flora is essential to support effective conservation strategies, which aim not only to guarantee the survival of the bees, but also to ensure the continued production of honey, a resource of great importance to local communities.