Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

An investigation of green space in a developing country city: The feasibility of creating a network of such spaces

<p>In developing countries a big issue for urban development is the growth in infrastructure in response to economic and population demands. Such development causes cities to expand and occupy the suburbs, turning them into more built up areas. The impacts of such urban growth are immediately observable in the reduction of green areas and environmental quality, and diminishing contact with the natural environment. This study will focus on green spaces in a city in a developing country to consider the effect of this urbanization. In response to urban growth in developed countries attempts have been made to link together green spaces into a form of networks. These networks are intended to conserve the function of natural areas in towns and cities while still accommodating development. The greenway or green network and ecological network are two successful approaches developed in America and Europe. This study assesses the green spaces in Makassar, an Indonesia city, to see possibility of implementing such concepts. The study begins by redefining spaces into a typology, then assessing the spaces through three stages. The first stage is biodiversity assessment. The Rapid Biodiversity Assessment, adapted from a study in the UK, is used to assess plant biodiversity as an indicator of the quality of green spaces in urban areas. This method was adjusted and simplified to reflect the limitation in resources and time. The second stage was assessment of spaces based on a target species, in this case urban birds. The third stage combines the biodiversity score with consideration of space size and ownership. This stage produced different classes of spaces. These stages produced three different maps which were then overlaid to find the best quality green spaces termed ‘the most preferred spaces’. The next step was to see whether these spaces could be linked up in a network and to determine what sort of network could be achieved. In this part of the analysis spaces are grouped into main patches and scattered small patches, termed stepping stones. With this approach the potential connectivity can be observed visually. This study also acknowledged the significance of areas of ecological quality outside the main city but within the greater urban region and proposed connection of the network of spaces outward towards two natural parks, which could be considered as the main ecological patches. Having assessed the two main elements of a green space network—patches and corridors—through visual observation of the maps generated by the fieldwork, this study concludes that currently an ecological network is not feasible for the city because of the condition of the green spaces that make up the patches and corridors. Even a greenway along the main river corridor is not currently feasible because the highly valuable natural remnants have been significantly fragmented by cultural activities. Similarly, the road corridors are also not currently in a promising condition. The thesis ends with recommendations for the improvement of these.</p>

An investigation of green space in a developing country city: The feasibility of creating a network of such spaces

<p>In developing countries a big issue for urban development is the growth in infrastructure in response to economic and population demands. Such development causes cities to expand and occupy the suburbs, turning them into more built up areas. The impacts of such urban growth are immediately observable in the reduction of green areas and environmental quality, and diminishing contact with the natural environment. This study will focus on green spaces in a city in a developing country to consider the effect of this urbanization. In response to urban growth in developed countries attempts have been made to link together green spaces into a form of networks. These networks are intended to conserve the function of natural areas in towns and cities while still accommodating development. The greenway or green network and ecological network are two successful approaches developed in America and Europe. This study assesses the green spaces in Makassar, an Indonesia city, to see possibility of implementing such concepts. The study begins by redefining spaces into a typology, then assessing the spaces through three stages. The first stage is biodiversity assessment. The Rapid Biodiversity Assessment, adapted from a study in the UK, is used to assess plant biodiversity as an indicator of the quality of green spaces in urban areas. This method was adjusted and simplified to reflect the limitation in resources and time. The second stage was assessment of spaces based on a target species, in this case urban birds. The third stage combines the biodiversity score with consideration of space size and ownership. This stage produced different classes of spaces. These stages produced three different maps which were then overlaid to find the best quality green spaces termed ‘the most preferred spaces’. The next step was to see whether these spaces could be linked up in a network and to determine what sort of network could be achieved. In this part of the analysis spaces are grouped into main patches and scattered small patches, termed stepping stones. With this approach the potential connectivity can be observed visually. This study also acknowledged the significance of areas of ecological quality outside the main city but within the greater urban region and proposed connection of the network of spaces outward towards two natural parks, which could be considered as the main ecological patches. Having assessed the two main elements of a green space network—patches and corridors—through visual observation of the maps generated by the fieldwork, this study concludes that currently an ecological network is not feasible for the city because of the condition of the green spaces that make up the patches and corridors. Even a greenway along the main river corridor is not currently feasible because the highly valuable natural remnants have been significantly fragmented by cultural activities. Similarly, the road corridors are also not currently in a promising condition. The thesis ends with recommendations for the improvement of these.</p>

Documenting trumpet leaf-miner moths (Tischeriidae): new Neotropical Coptotriche and Astrotischeria species, with notes on Sapindaceae as a host-plant family

Four new species of trumpet leaf-miner moths (Tischeriidae) are described from the Neotropics: Coptotriche serjaniphaga Remeikis & Stonis, sp. nov., feeding on Serjania Mill. (Sapindaceae), Astrotischeria mystica Diškus & Stonis, sp. nov., feeding on Verbesina L. (Asteraceae), A. yungasi Diškus & Stonis, sp. nov., feeding on Oyedaea DC. (Asteraceae), and A. parapallens Diškus & Stonis, sp. nov., feeding on Baccharis L. (Asteraceae). Records on Sapindaceae-feeding Tischeriidae are very rare and Serjania is a novel host-plant genus for Tischeriidae. It is hypothesized that Serjania, a diverse genus in the tropical and subtropical Americas, may be a host for many undiscovered species of specialized stenophagous Tischeriidae. The new species are illustrated with photographs of the adults, male and, if available, female genitalia, and the leaf mines. We briefly discuss the importance of new species descriptions as a part of biodiversity assessment.

Análisis de la superposición del mapa de superficie agrícola con áreas de importancia para la biodiversidad en 10 departamentos del Perú

La seguridad alimentaria requiere de sistemas estadísticos que les permitan producir información agrícola y rural adecuada, en ese sentido, el Ministerio de Desarrollo Agrario y Riego - MIDAGRI, publica el 21 de diciembre del 2020 la Resolución Ministerial 0322-2020-MIDAGRI, en ella alude a la estrategia de la FAO mencionando la necesidad de vincular las dimensiones económicas, sociales y ambientales para monitorear el uso de la tierra. En este artículo, se analiza preliminarmente la vinculación de la dimensión económica y ambiental en 10 departamentos del Perú, superponiendo el Mapa Nacional de Superficie Agrícola, publicado por el MIDAGRI sobre las áreas de importancia para la biodiversidad. Con el se ha usado como fuente la información Integrated Biodiversity Assessment Tool – IBAT que reúne varias categorías relativas a las áreas de importancia para la biodiversidad. El resultado del análisis arrojó que en los 10 departamentos evaluados la superficie agrícola se superpone con áreas RAMSAR y AZE en 7% y 5% respectivamente, las áreas KBA, IBA, Reservas de Biósfera y ecosistemas frágiles tiene valores menores al 5%. Finalmente, se concluye que es necesario realizar el análisis en los restantes departamentos del Perú para obtener una estimación a nivel nacional.