Why vouchers matter in botanical research

Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility

BACKGROUND

There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications.

RESULTS

In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis.

CONCLUSIONS

The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5 mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.

Photographs as an essential biodiversity resource: drivers of gaps in the vascular plant photographic record

The photographic record is increasingly becoming an important biodiversity resource for primary research and conservation monitoring. However, globally, there are important gaps in this record even in relatively well-researched floras. To quantify the gaps in the Australian native vascular plant photographic record, we systematically surveyed 33 sources of well-curated species photographs, assembling a list of species with accessible and verifiable photographs, as well as the species for which this search failed. Of 21 077 Australian native species, 3715 lack a verifiable photograph across our 33 surveyed resources. There are three major geographic hotspots of unphotographed species in Australia, all far from current population centres. Many unphotographed species are small in stature or uncharismatic, and many are also recently described. The large number of recently described species without accessible photographs was surprising. There are longstanding efforts in Australia to organise the plant photographic record, but in the absence of a global consensus to treat photographs as an essential biodiversity resource, this has not become common practice. Many recently described species are small-range endemics and some have special conservation status. Completing the botanical photographic record across the globe will facilitate a virtuous feedback loop of more efficient identification, monitoring and conservation.

Building More Resilient Culture Collections: A Call for Increased Deposits of Plant-Associated Bacteria

Biological collections preserve our past, while helping protect our future and increase future knowledge. Plant bacterial culture collections are our security for domestic and global biosecurity. This feature article will provide an introduction to the global position of plant bacterial collections. The role of collections in monitoring plant pathogenic bacteria will be explored through the presentation of five cases studies. These case studies demonstrate why culture collections were imperative for the outcome in each situation. We discuss what we believe should be the best practices to improve microbial preservation and accessioning rates, and why plant bacterial culture collections must increase deposits to be prepared for future emerging pathogens. This is not only the case for global culture collections, but on a much bigger scale, our future scientific successes, our biosecurity decisions and responses, and our knowledge are contingent upon preserving our valuable bacterial strains. It is hoped that once you read this article, you will see the need to deposit your strains in registered public collections and make a concerted effort to build better bacterial culture collections with us.

Flippant attitudes towards plant identification jeopardize early career botanists

Early career botanists are under threat due to a current misunderstanding of some of their scientific skills, inviting pervasive professional intrusion and leading to a denial of scientific credit. Measures need to be taken to curb this erosion of the discipline, including flagging bad practice, disclosing responsibilities, and upholding scientific credit.

A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo)

Persistent identifiers (PID) to identify digital representations of physical specimens in natural science collections (i.e., digital specimens) unambiguously and uniquely on the Internet are one of the mechanisms for digitally transforming collections-based science. Digital Specimen PIDs contribute to building and maintaining long-term community trust in the accuracy and authenticity of the scientific data to be managed and presented by the Distributed System of Scientific Collections (DiSSCo) research infrastructure planned in Europe to commence implementation in 2024. Not only are such PIDs valid over the very long timescales common in the heritage sector but they can also transcend changes in underlying technologies of their implementation. They are part of the mechanism for widening access to natural science collections. DiSSCo technical experts previously selected the Handle System as the choice to meet core PID requirements.

Using a two-step approach, this options appraisal captures, characterises and analyses different alternative Handle-based PID schemes and the possible operational modes of use. In a first step a weighting and ranking the options has been applied followed by a structured qualitative assessment of social and technical compliance across several assessment dimensions: levels of scalability, community trust, persistence, governance, appropriateness of the scheme and suitability for future global adoption. The results are discussed in relation to branding, community perceptions and global context to determine a preferred PID scheme for DiSSCo that also has potential for adoption and acceptance globally.

DiSSCo will adopt a ‘driven-by DOI’ persistent identifier (PID) scheme customised with natural sciences community characteristics. Establishing a new Registration Agency in collaboration with the International DOI Foundation is a practical way forward to support the FAIR (findable, accessible interoperable, reusable) data architecture of DiSSCo research infrastructure. This approach is compatible with the policies of the European Open Science Cloud (EOSC) and is aligned to existing practices across the global community of natural science collections.

Validation of a Triplex Quantitative Polymerase Chain Reaction Assay for Detection and Quantification of Traditional Protein Sources, Pisum sativum L. and Glycine max (L.) Merr., in Protein Powder Mixtures

Several botanicals have been traditionally used as protein sources, including the leguminous Pisum sativum L. and Glycine max (L.) Merr. While a rich history exists of cultivating these plants for their whole, protein-rich grain, modern use as powdered supplements present a new challenge in material authentication. The absence of clear morphological identifiers of an intact plant and the existence of long, complex supply chains behoove industry to create quick, reliable analytical tools to identify the botanical source of a protein product (many of which contain multiple sources). The utility of molecular tools for plant-based protein powder authentication is gaining traction, but few validated tools exist. Multiplex quantitative polymerase chain reaction (qPCR) can provide an economical means by which sources can be identified and relative proportions quantified. We followed established guidelines for the design, optimization, and validation of qPCR assay, and developed a triplex qPCR assay that can amplify and quantify pea and soy DNA targets, normalized by a calibrator. The assay was evaluated for analytical specificity, analytical sensitivity, efficiency, precision, dynamic range, repeatability, and reproducibility. We tested the quantitative ability of the assay using pea and soy DNA mixtures, finding exceptional quantitative linearity for both targets - 0.9983 (p < 0.0001) for soy and 0.9915 (p < 0.0001) for pea. Ratios based on mass of protein powder were also tested, resulting in non-linear patterns in data that suggested the requirement of further sample preparation optimization or algorithmic correction. Variation in fragment size within different lots of commercial protein powder samples was also analyzed, revealing low SD among lots. Ultimately, this study demonstrated the utility of qPCR in the context of protein powder mixtures and highlighted key considerations to take into account for commercial implementation.

Traditional usage and biological activity of Plectranthus madagascariensis and its varieties: A review

ETHNOPHARMACOLOGICAL RELEVANCE

Plectranthus madagascariensis (Pers.) Benth. is an indigenous aromatic South African plant species that are traditionally used to treat various dermatological and respiratory ailments.

AIM OF THE STUDY

Three varieties of P. madagascariensis exist in South Africa, namely, Plectranthus aliciae (Codd) van Jaarsv. & T.J. Edwards, Plectranthus ramosior (Benth.) Van Jaarsv. and Plectranthus madagascariensis (Pers.) Benth var. madagascariensis. This article summarizes the documented ethnobotanical uses and research which has been conducted to date on the chemical constituents and biological effects of P. madagascariensis and its varieties. This review aimed to investigate and highlight the lack scientific reports of the potential activity of these varieties based on their traditional usage and to emphasise the need for further investigation of the benefits of P. madagascariensis and its varieties.

MATERIALS AND METHODS

Extensive database retrieval using platforms not limited to but including Google Scholar, ScienceDirect and PubMed, was performed by using keywords such as "Plectranthus madagascariensis" "Plectranthus madagascariensis var. aliciae", "Plectranthus aliciae", "Plectranthus ramosior", "Plectranthus madagascariensis var. ramosior" and "Plectranthus hirtus" In addition, relevant books and digital documentation were consulted to collect all available scientific literature to provide a comprehensive review.

RESULTS

Several studies have reported the traditional usage of P. madagascariensis for the treatment of diseases related to the respiratory system such as coughs, colds and asthma as well as dermatological disorders associated with wounds and inflammation. Whilst there are no reports on the traditional usage of P. madagascariensis varieties to treat other maladies, several other species within the genus are used in other traditional practices. Plectranthus ramosior is used as a toxin for fishing. In literature, seven major phytochemical compounds have been identified from P. madagascariensis. Its extract and essential oil contain polyphenols, abietane diterpenes and abietane diterpenes with a quinone moiety. The extracts and major chemical constituents of P. madagascariensis and its major phytochemicals have reported activity against several biological targets. Reports relating to the antibacterial activity of P. madagascariensis against microbes associated with tuberculosis and wound infections has been consistent and correlates with the documented traditional usage of the plant. Literature reported on the antibacterial activity of P. aliciae targeting bacteria associated with wound infections and lung cancer cells. No further literature reports of the biological activity of the other P. madagascariensis varieties have been found. Other noteworthy biological activities reported in the literature of P. madagascariensis and its compounds include their activities against targets of Alzheimer's disease and breast cancer, in particular. This activity is not related to the traditional usage of the plant.

CONCLUSION

Plectranthus madagascariensis and its compounds have been proven to be effective in treating a range of maladies. Based on the extensive literature on this plant, it can be concluded that numerous in vitro pharmacological activities of P. madagascariensis have been reported. However, there is a lack of information available for this species with regards to its in vivo data including both pre-clinical and clinical studies. Since the extract of P. madagascariensis and its isolated compounds have displayed noteworthy anticancer potential, we recommend further investigation of pharmacokinetic studies to be included in future research.

How FAIR are plant sciences in the twenty-first century? The pressing need for reproducibility in plant ecology and evolution

The need for open, reproducible science is of growing concern in the twenty-first century, with multiple initiatives like the widely supported FAIR principles advocating for data to be Findable, Accessible, Interoperable and Reusable. Plant ecological and evolutionary studies are not exempt from the need to ensure that the data upon which their findings are based are accessible and allow for replication in accordance with the FAIR principles. However, it is common that the collection and curation of herbarium specimens, a foundational aspect of studies involving plants, is neglected by authors. Without publicly available specimens, huge numbers of studies that rely on the field identification of plants are fundamentally not reproducible. We argue that the collection and public availability of herbarium specimens is not only good botanical practice but is also fundamental in ensuring that plant ecological and evolutionary studies are replicable, and thus scientifically sound. Data repositories that adhere to the FAIR principles must make sure that the original data are traceable to and re-examinable at their empirical source. In order to secure replicability, and adherence to the FAIR principles, substantial changes need to be brought about to restore the practice of collecting and curating specimens, to educate students of their importance, and to properly fund the herbaria which house them.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

Vascular Plant Herbarium at the Kandalaksha Strict Nature Reserve (KAND), Russia

BACKGROUND

The present-day demand for digital availability of distributional data in biodiversity studies requires a special effort in assembling and editing the data otherwise scattered in paper literature and herbarium collections, which can be poorly accessible or little understood to present-day users and especially automatic data processors. Our project on developing the information resource for the vascular plant flora of Murmansk Region, Russia, includes processing and making digitally available all the data on the taxonomy and distribution of this flora. So far, published distribution maps are limited to the old set in the Flora of Murmansk Region (published in 1953-1966) and the Red Data Book of Murmansk Region (ed. 2, published in 2014). These publications did not take into account the main part of the herbarium collections kept at the Kandalaksha Strict Nature Reserve, which are the basis for numerous local publications that appear scattered and, therefore, little accessible nowadays.

NEW INFORMATION

We present a complete dataset of all holdings of vascular plants in the Herbarium of the Kandalaksha Strict Nature Reserve, totalling 10,218 specimens collected during 1947-2019, which are referable to 764 species and 19 subspecies. All specimens were georeferenced with the utmost precision available. This dataset offers a complete and dense coverage of the Nature Reserve's territory (islands and adjacent mainland coastal areas of the Barents and White Seas, Murmansk Region and Republic of Karelia, Russia); these data are little represented in herbarium collections elsewhere.

Bioprospecting for Antibacterial Drugs: a Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls

Bioprospecting is the exploration, extraction and screening of biological material and sometimes indigenous knowledge to discover and develop new drugs and other products. Most antibiotics in current clinical use (eg. β-lactams, aminoglycosides, tetracyclines, macrolides) were discovered using this approach, and there are strong arguments to reprioritize bioprospecting over other strategies in the search for new antibacterial drugs. Academic institutions should be well positioned to lead the early stages of these efforts given their many thousands of locations globally and because they are not constrained by the same commercial considerations as industry. University groups can lack the full complement of knowledge and skills needed though (eg. how to tailor screening strategy to biological source material). In this article, we review three key aspects of the bioprospecting literature (source material and in vitro antibacterial and toxicity testing) and present an integrated multidisciplinary perspective on (a) source material selection, (b) legal, taxonomic and other issues related to source material, (c) cultivation methods, (d) bioassay selection, (e) technical standards available, (f) extract/compound dissolution, (g) use of minimum inhibitory concentration and selectivity index values to identify progressible extracts and compounds, and (h) avoidable pitfalls. The review closes with recommendations for future study design and information on subsequent steps in the bioprospecting process.

Fritillariae Thunbergii Bulbus: Traditional Uses, Phytochemistry, Pharmacodynamics, Pharmacokinetics and Toxicity

Fritillariae Thunbergii Bulbus (FTB) has been widely used as an antitussive herb for thousands of years in China. However, FTB's traditional uses, chemical compounds and pharmacological activities have not been systematically reviewed. This study aimed to review its traditional uses, phytochemistry, pharmacodynamics, pharmacokinetics and toxicity. We searched the Encyclopedia of Traditional Chinese Medicine to explore the historical records which indicate that it acts to clear heat, resolve phlegm, relieve cough, remove toxicity and disperse abscesses and nodules. We searched 11 databases to identify potential phytochemical or pharmacological studies. Characteristics of its chemical constituents, pharmacological effects, pharmacokinetic and toxicity were descriptively summarized. A total of 9706 studies were identified and 83 of them were included. As a result, 134 chemical constituents were identified, including 26 alkaloids, 29 compounds found in essential oils, 13 diterpenoids, two carbohydrates, two sterols, 18 amino acids, six nucleosides, four nucleobases, four fatty acids, three lignans, and 27 elements. Thirteen pharmacological effects of FTB were identified, including anti-cancer, tracheobronchial relaxation, antitussive, expectorant, anti-muscarinic, anti-inflammation, anti-thyroid, regulation of blood rheology, antiulcer, anti-diarrhea, pain suppression, antioxidation and neuroprotection. These pharmacological activities may be mainly attributed to the alkaloids in FTB. Further phytochemical, pharmacological and network pharmacological studies are recommended.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Non-Destructive Chemical Analysis of a Garcinia mangostana L. (Mangosteen) Herbarium Voucher Specimen

Herbarium voucher specimens are used primarily for taxonomic confirmation. However, they also afford a record of the metabolic profile of a plant, potentially at the time it was collected, or at the very least, at the time of analysis. Even with the enhanced sensitivity of modern analytical techniques, analysis of the metabolites of a herbarium voucher requires removal and consumption of at least part of an entire specimen. We present herein a non-destructive method to analyze the metabolites of herbarium voucher specimens with the droplet-liquid microjunction-surface sampling probe (droplet probe) coupled to ultra-performance liquid chromatography and highresolution mass spectrometry. As proof of concept, a herbarium voucher specimen of Garcinia mangostana (mangosteen) was utilized due to the well-characterized xanthones biosynthesized by this plant, which are of interest as potential anticancer agents. Also, the juice of the fruits of this plant is used widely in the United States and in other countries as a botanical dietary supplement. Metabolite profiles of the sampled surfaces were compared to a subset of xanthone standards. Using this innovative method on the herbarium voucher specimen, we were able to readily identify cytotoxic prenylated xanthones while maintaining the integrity of the entire specimen.

iNaturalist as a tool to expand the research value of museum specimens

PREMISE OF THE STUDY

Innovative approaches to specimen collection and curation are needed to maximize the utility of natural history collections in a new era of data use. Associated data, such as digital images from the field, are routinely collected with recent herbarium specimens. However, these data often remain inaccessible and are rarely curated alongside the associated physical specimens, which limits future data use.

METHODS AND RESULTS

We leveraged the widely used citizen science platform, iNaturalist, to permanently associate field-collected data to herbarium specimens, including information not well preserved in traditional specimens. This protocol improves the efficiency and accuracy of all steps from the collecting event to specimen curation and enhances the potential uses of specimens.

CONCLUSIONS

iNaturalist provides a standardized and cost-efficient enhancement to specimen collection and curation that can be easily adapted for specific research goals or other collection types beyond herbaria.

Integrated analytical assets aid botanical authenticity and adulteration management

This article reviews and develops a perspective for the meaning of authenticity in the context of quality assessment of botanical materials and the challenges associated with discerning adulterations vs. contaminations vs. impurities. Authentic botanicals are by definition non-adulterated, a mutually exclusive relationship that is confirmed through the application of a multilayered set of analytical methods designed to validate the (chemo)taxonomic identity of a botanical and certify that it is devoid of any adulteration. In practice, the ever-increasing sophistication in the process of intentional adulteration, as well as the growing number of botanicals entering the market, altogether necessitate a constant adaptation and reinforcement of authentication methods with new approaches, especially new technologies. This article summarizes the set of analytical methods - classical and contemporary - that can be employed in the authentication of botanicals. Particular emphasis is placed on the application of untargeted metabolomics and chemometrics. An NMR-based untargeted metabolomic model is proposed as a rapid, systematic, and complementary screening for the discrimination of authentic vs. potentially adulterated botanicals. Such analytical model can help advance the evaluation of botanical integrity in natural product research.

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost-effective generation of high-quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.

Contrasting spatial, temporal and environmental patterns in observation and specimen based species occurrence data

Species occurrence data records the location and time of an encounter with a species, and is valuable for many aspects of ecological and evolutionary analyses. A key distinction within species occurrence data is between (1) collected and preserved specimens that can be taxonomically validated (i.e., natural history collections), and (2) observations, which are more error prone but richer in terms of number and spread of observations. In this study we analyse the distribution in temporal, spatial, taxonomic and environmental coverage of specimen- and observation based species occurrence data for land plants in Norway, a region with strong climatic and human population density gradients. Of 4.8 million species occurrence records, the majority (78%) were observations. However, there was a greater species richness in the specimen record (N = 4691) than in the observation record (N = 3193) and most species were recorded more as specimens than observations. Specimen data was on average older, and collected later during the year. Both record types were highly influenced by a small number of prolific contributors. The species most highly represented in the observation data set were widespread or invasive, while in the specimen records, taxonomically challenging species were overrepresented. Species occurrence records were unevenly spatially distributed. Both specimen and observation records were concentrated in regions of Norway with high human population density and with high temperatures and precipitation, but in different regions within Norway. Observation and specimen records thus differ in taxonomic, temporal, spatial and environmental coverage for a well-sampled group and study region, potentially influencing the ecological inferences made from studies utilizing species occurrence data. The distribution of observation data dominates the dataset, so inferences of species diversity and distributions do not correspond to the evolutionary or physiological knowledge of species, which is based on specimen data. We make recommendations for users of biodiversity data, and collectors to better exploit the complementary strengths of these distinct biodiversity data types.

Herbarium data: Global biodiversity and societal botanical needs for novel research

Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non-traditional digitized data fields, user annotation capability, and born-digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision-making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.

Phytochemical screening and biological activity of Lamiaceae family plant extracts

The current study aimed to investigate ethanolic extracts from the following medicinal plant species cultivated in western Romania: Melissa officinalis L., Rosmarinus officinalis L. (RO) and Salvia officinalis L. (SO). Antioxidant activity, total phenolics content and a profile of the main hydroxycinnamic acids (HCAs), including caffeic, ferulic, coumaric and rosmarinic acids, was determined for each plant extract. The in vitro antimicrobial activity against four bacterial strains (Escherichia coli, Listeria-, Pseudomonas aeruginosa and Staphylococcus aureus), and the effect on cell viability in two melanoma cell lines (B164A5 murine melanoma and A375 human melanoma) was also assessed. The results indicated that total phenolics content was 73.76-274.73 mg GAE·g-1 and the antioxidant activity was 2.32-2.87 mM Fe2+·100 g-1. There was found a strong positive correlation (R=0.9691) between total phenolics content and the antioxidant activity in the investigated samples. Regarding the HCA profile obtained by high performance liquid chromatography, the results demonstrated that rosmarinic acid represents the main identified compound. The ethanolic extracts of RO and SO exhibited antibacterial activity against Gram positive and Gram negative bacteria. RO was the most effective in terms of decreasing the cell viability of murine and human melanoma cell lines, while the HCAs did not exhibit any effect on cell viability. These findings suggest that plant extracts from the Lamiaceae family may used in the clinic as natural antibacterial agents.

The NCBI BioCollections Database

The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses. The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections

Toward a service-based workflow for automated information extraction from herbarium specimens

Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses. The evolving system presently covers the generation of optical character recognition (OCR) from specimen images, the identification of regions of interest in images and the extraction of meaningful information items from OCR. These implementations were developed as part of the Deutsche Forschungsgemeinschaft-funded a standardised and optimised process for data acquisition from digital images of herbarium specimens (StanDAP-Herb) Project.

The frontier of data discoverability: Why we need to share our data

We are now in an era where sharing and making data widely accessible are not only expected within many disciplines, but also required by federal granting agencies and many scientific journals. In addition, there are practical reasons why authors should deposit their data into permanent data repositories: (1) it prevents data loss due to accidents, theft, or death of the researcher; (2) it enables published research to be reproduced by others; (3) publications associated with accessible data sets can have higher citation rates; (4) deposited data sets are increasingly recognized for scholarly recognition and professional advancement; and (5) stored and accessible data can be used in the future for projects that are unanticipated today. Applications in Plant Sciences requires that data underlying its articles be publicly accessible as a condition of publication to promote the continued advancement of the field of plant biology.

Temporal degradation of data limits biodiversity research

Spatial and/or temporal biases in biodiversity data can directly influence the utility, comparability, and reliability of ecological and evolutionary studies. While the effects of biased spatial coverage of biodiversity data are relatively well known, temporal variation in data quality (i.e., the congruence between recorded and actual information) has received much less attention. Here, we develop a conceptual framework for understanding the influence of time on biodiversity data quality based on three main processes: (1) the natural dynamics of ecological systems—such as species turnover or local extinction; (2) periodic taxonomic revisions, and; (3) the loss of physical and metadata due to inefficient curation, accidents, or funding shortfalls. Temporal decay in data quality driven by these three processes has fundamental consequences for the usage and comparability of data collected in different time periods. Data decay can be partly ameliorated by adopting standard protocols for generation, storage, and sharing data and metadata. However, some data degradation is unavoidable due to natural variations in ecological systems. Consequently, changes in biodiversity data quality over time need be carefully assessed and, if possible, taken into account when analyzing aging datasets.

Mismatch of morphological and molecular identifications in native and invasive subspecies of Codium fragile (Bryopsidophyceae, Chlorophyta)

Several subspecies are defined within Codium fragile, including the invasive C. fragile ssp. fragile, first reported in New Zealand in 1973. An endemic subspecies, C. fragile ssp. novae-zelandiae, is also found throughout New Zealand. The two subspecies exhibit morphological and molecular variation, although these have never been evaluated together. We compared variation between subspecies at locations in Auckland, identifying subspecies using rps3-rpl16 DNA sequence data, and assessing gross morphological differences, anatomical utricle characters and morphometrics. The taxonomic utility of the morphometric data sets was assessed by linear discriminant analysis. Utricle characters and measurements varied within individual thalli and between different preservation methods. The phenotypes of both subspecies were highly variable and influenced by environment. Accurate subspecies delimitation using morphological data was not possible; the discriminant analyses performed no better than chance for all combinations of the morphological data. Specimens from New Zealand, Canada, Australia and Ireland were sequenced using both the rps3-rpl16 and tufA plastid markers. The tufA elongation factor was shown to be a good candidate for differentiating subspecies of C. fragile. This marker is twice the length of the rps3-rpl16 spacer, shows greater variation between ssp. fragile and novae-zelandiae, and is less prone to sequencing error. A simple restriction enzyme digest of the tufA amplicon can distinguish ssp. fragile and ssp. novae-zelandiae. Our study expands the known range of the ssp. fragile in New Zealand, including the first record of this subspecies from the west coast of Auckland, and points to a need to re-evaluate morphological and molecular criteria for subspecies currently defined within C. fragile.