Going down the rabbit hole: insight into the future of Paramecium (Ciliophora, Protista) biodiversity surveys DOI Open Access
Sebastian Tarcz

Folia Biologica, Год журнала: 2024, Номер 72(4), С. 130 - 142

Опубликована: Дек. 31, 2024

Paramecium , a research subject in many areas of life sciences, appeared to be ciliate genus with well known biodiversity structure. However, the understanding its biological diversity has been evolving rapidly recent years, driven by discovery new taxa and an expanded knowledge distribution species. Most future insights into are expected come from molecular data, particularly through eDNA sampling. As one most recognisable microeukaryotes, commonly found freshwater ecosystems, over century – including extensive reference data GenBank records living culture collections holds significant potential become model for studies biogeography. This review addresses challenges species identification within genus, current state on other factors that may shape research. Despite some existing bottlenecks, approaches acquisition analysis will enable researchers integrate diverse lines evidence, allowing exceptional explorations populations.

Язык: Английский

Towards a toolkit for global insect biodiversity monitoring DOI Creative Commons
Roel van Klink, Julie Koch Sheard, Toke T. Høye

и другие.

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1904)

Опубликована: Май 5, 2024

Insects are the most diverse group of animals on Earth, yet our knowledge their diversity, ecology and population trends remains abysmally poor. Four major technological approaches coming to fruition for use in insect monitoring ecological research—molecular methods, computer vision, autonomous acoustic radar-based remote sensing—each which has seen advances over past years. Together, they have potential revolutionize ecology, make all-taxa, fine-grained feasible across globe. So far, within among technologies largely taken place isolation, parallel efforts projects led redundancy a methodological sprawl; yet, given commonalities goals approaches, increased collaboration integration could provide unprecedented improvements taxonomic spatio-temporal resolution coverage. This theme issue showcases recent developments state-of-the-art applications these technologies, outlines way forward regarding data processing, cost-effectiveness, meaningful trend analysis, open requirements. papers set stage future automated monitoring. article is part ‘Towards toolkit global biodiversity monitoring’.

Язык: Английский

Процитировано

15
Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices DOI Creative Commons
Rosetta C. Blackman, Luca Carraro, François Keck

и другие.

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1904)

Опубликована: Май 5, 2024

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they strongly affected by anthropogenic activities. As of these taxa highly sensitive to environmental change, offer particularly good early warning system for human-induced thus leading their intense monitoring. In ecosystems there is plethora biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported freshwater alone. Ultimately, macroinvertebrates used calculate ecological indices describing the state systems. Many not only hard compare, but especially difficult scale in time space. Novel DNA-based approaches measure change environments now unprecedented opportunities, also possible integration towards commonly applicable indices. Here, we first give perspective on organisms, focus insects, how move beyond traditional point-based Second, demonstrate proof-of-concept spatially upscaling based DNA, demonstrating novel molecular hydrological models allows an accurate evaluation at catchment scale. This article part theme issue ‘Towards toolkit global biodiversity monitoring’.

Язык: Английский

Процитировано

9
Three steps towards comparability and standardization among molecular methods for characterizing insect communities DOI Creative Commons
Elzbieta Iwaszkiewicz‐Eggebrecht, Vera Zizka, Christina Lynggaard

и другие.

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1904)

Опубликована: Май 5, 2024

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based large-scale monitoring, to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, provide three recommendations how harmonize efforts biodiversity assessment monitoring via metabarcoding: (i) should adopt use synthetic spike-ins, which will act as positive controls internal standards; (ii) consider using several markers through a multiplex polymerase chain reaction (PCR) approach; (iii) commit publication transparency all protocol-associated metadata standardized fashion. For (i), ready-to-use recipe cytochrome

Язык: Английский

Процитировано

8
Delivering on a promise: futureproofing automated insect monitoring methods DOI
Roel van Klink

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2024, Номер 379(1904)

Опубликована: Май 5, 2024

Due to rapid technological innovations, the automated monitoring of insect assemblages comes within reach. However, this continuous innovation endangers methodological continuity needed for calculating reliable biodiversity trends in future. Maintaining over prolonged periods time is not trivial, since technology improves, reference libraries grow and both hard- software used now may no longer be available Moreover, because data on many species are collected at same time, there will simple way calibrating outputs old new devices. To ensure that long-term can calculated using data, I make four recommendations: (1) Construct devices last decades, have a five-year overlap period when replaced. (2) resemble ones, especially some kind attractant (e.g. light) used. Keep extremely detailed metadata collection, detection identification methods, including attractants, enable this. (3) Store raw (sounds, images, DNA extracts, radar/lidar detections) future reprocessing with updated classification systems. (4) Enable forward backward compatibility processed example by in-silico 'degradation' match older quality. This article part theme issue 'Towards toolkit global monitoring'.

Язык: Английский

Процитировано

5
The transformative potential of eDNA-based biodiversity impact assessment DOI Creative Commons
Emma Granqvist, Robert M. Goodsell, Mats Töpel

и другие.

Current Opinion in Environmental Sustainability, Год журнала: 2025, Номер 73, С. 101517 - 101517

Опубликована: Март 11, 2025

Язык: Английский

Процитировано

0
Methodologies for the identification of historic forest pathogen dynamics DOI
Matthew H. Watkins, Sofía Consuegra, Stephan Woodborne

и другие.

The Holocene, Год журнала: 2025, Номер unknown

Опубликована: Апрель 11, 2025

The scale, severity, and synchronicity of recent outbreaks forest pests such as bark beetles (Coleoptera, Scolytinae) defoliators (Lepidoptera, Choristoneura) within coniferous ecosystems North America, Europe, Asia are widely regarded ‘unprecedented’. Despite devastating outbreak occurrence in times, very little is known about historic occurrence. Traditional methods reconstructing dynamics, including dendroecology, pollen analysis, the identification fossilised pest remains, all have critical weaknesses their ability to reconstruct accurately, notably non-standardised methodologies, varying parameters for identifying periods proxy records, a bias towards detection large-scale, highly destructive only. development more accurate tool dynamics palaeoecological record has been prioritised one top 50 areas research Quaternary science. This paper assesses current before presenting potential role DNA-based methodologies can play overcoming some these limitations providing comprehensive reconstructions, critically, direct pathogen outbreaks.

Язык: Английский

Процитировано

0
A morphological and high throughput sequencing workflow to identify Australian ants (Hymenoptera, Formicidae): a new tool for biosecurity and biodiversity DOI Creative Commons
Francesco Martoni, James T. Buxton,

KATHRYN S. SPARKS

и другие.

Metabarcoding and Metagenomics, Год журнала: 2024, Номер 8

Опубликована: Окт. 21, 2024

Ants are often the most ubiquitous and ecologically influential components of terrestrial systems, exhibiting an exceptionally high level endemic diversity. Simultaneously, exotic ants can be amongst environmentally economically devastating biological invaders. Distinguishing between related natives is essential for early detection to reduce chance establishment, but at species-level there remains a great deal uncertainty among several diverse, widespread dominant genera. This taxonomic impediment negatively impacts use molecular techniques relying on reference databases, due poor state ant DNA sequences in publicly available repositories, with many species not represented all others incorrectly identified. As result, biosecurity screening targeted assigning identifications biodiversity remain two separate areas focus Australia. Here we propose workflow identification that enables simultaneous processing large numbers “bulk” samples each containing individuals, increasing resolution assignment, generating curated database linked voucher specimens. We non-destructive extraction method compare throughput sequencing (HTS) metabarcoding platforms – MiSeq (Illumina) MinION (Oxford Nanopore Technologies) up 180 bulk mixed per run. approach allowed acquisition from specimens morphologically examined by expert taxonomists. work highlights advantages current limitations DNA-based identifications, needs standardisation, as well importance taxonomy-based curation both biosecurity.

Язык: Английский

Процитировано

1
Going down the rabbit hole: insight into the future of Paramecium (Ciliophora, Protista) biodiversity surveys DOI Open Access
Sebastian Tarcz

Folia Biologica, Год журнала: 2024, Номер 72(4), С. 130 - 142

Опубликована: Дек. 31, 2024

Paramecium , a research subject in many areas of life sciences, appeared to be ciliate genus with well known biodiversity structure. However, the understanding its biological diversity has been evolving rapidly recent years, driven by discovery new taxa and an expanded knowledge distribution species. Most future insights into are expected come from molecular data, particularly through eDNA sampling. As one most recognisable microeukaryotes, commonly found freshwater ecosystems, over century – including extensive reference data GenBank records living culture collections holds significant potential become model for studies biogeography. This review addresses challenges species identification within genus, current state on other factors that may shape research. Despite some existing bottlenecks, approaches acquisition analysis will enable researchers integrate diverse lines evidence, allowing exceptional explorations populations.

Язык: Английский

Процитировано

0