Journal of Threatened Taxa |
www.threatenedtaxa.org | 26 July 2023 | 15(7): 23587–23595
ISSN 0974-7907
(Online) | ISSN 0974-7893 (Print)
https://doi.org/10.11609/jott.8081.15.7.23587-23595
#8081 | Received 30
June 2022 | Final received 16 May 2023 | Finally accepted 20 June 2023
Developing a fast, reproducible,
and simple protocol for virtual lichen herbarium using barcoding and QR code
techniques
S. Jeya
Preethi 1 & P. Ponmurugan 2
1,2 Biomedical Research Laboratory,
Department of Botany, Bharathiar University,
Coimbatore, Tamil Nadu 641046, India.
1 jeyapreethiselvam@gmail.com, 2
drponmurugan@gmail.com (corresponding author)
Abstract: In recent days, biological specimens are digitalized and
digital images are available in virtual herbarium for teaching and learning
process. Now, there is a need to explore possibilities of usage of barcodes and
quick response (QR) codes in developing virtual herbarium for quick access as
well as study the taxonomy of repository specimens. In order to establish a
virtual herbarium for lichens using barcode and QR code techniques, lichen
specimens such as Chrysothrix candelaris (L.) J.R.Laundon,
Leucodermia leucomelos (L.)
Kalb, Heterodernia flabellate (fee) D.D.Awasthi, Parmotrema andinum (Mull.Arg.) Hale, Parmotrema grayanum (Hue)
Hale, Parmellinella stuppeum
(Taylor) Hale, and Ramalina
intermedia (Delise ex Nyl.)
Nyl. were collected from the Eastern Ghats and
the Western Ghats of Tamil Nadu, India and were identified based on
morphological, anatomical and biochemical methods. Moreover, these specimens
were preserved in the conventional lichen herbarium as reference materials for
future studies. The barcodes and QR codes were generated for all the repository
specimens to access the materials as well as to get a complete description of
the lichen specimens. The generated barcodes provided the binomial name of
lichen specimens along with their accession number. Similarly, the QR codes
provided the digital image of lichen specimens along with complete descriptions
such as distribution, habit and habitat, growth forms, name of the family,
reproductive structure, chemistry, nature of thallus structure and lichen
secondary metabolites. From these studies, we standardized a simple, rapid with
reproducible protocol to develop a virtual herbarium for lichens to get the
digital image and to access the complete descriptions of lichen specimens. This
study might be useful for Lichenologists to get information about lichens in
digital form and to maintain the lichen wealth for future regenerations without
disturbing the lichen biodiversity.
Keywords: Barcodes, conventional lichen herbarium, digital images,
lichen biodiversity, QR codes, quick access, repository, specimens.
Editor: Anonymity requested. Date of publication: 26 July 2023 (online &
print)
Citation:
Preethi, S.J. & P. Ponmurugan (2023). Developing a
fast, reproducible, and simple protocol for virtual lichen herbarium using
barcoding and QR code techniques. Journal of Threatened Taxa 15(7): 23587–23595. https://doi.org/10.11609/jott.8081.15.7.23587-23595
Copyright: © Preethi & Ponmurugan 2023. Creative Commons Attribution 4.0
International License. JoTT allows unrestricted use, reproduction, and
distribution of this article in any medium by providing adequate credit to the
author(s) and the source of publication.
Funding: This work was supported by the Bharathiar University and Rashtriya Uchchatar Shiksha Abhiyan (RUSA 2.0) - Bharathiar Cancer Theranostics Research Centre, Coimbatore, Tamil Nadu, India.
Competing interests: The authors declare no competing interests.
Author details: Jeya Preethi Selvam,
research scholar, Biomedical Research Laboratory, Department of Botany, Bharathiar University, Coimbatore, Tamil Nadu. Dr. P. Ponmurugan, associate professor, Department of Botany, Bharathiar University, Coimbatore, Tamil Nadu.
Author contributions: The concept plan and manuscript editing and modification were done by the corresponding author Dr. P. Ponmurugan and the manuscript writing were done by the first author Ms. S. Jeya Preethi.
Acknowledgements: The authors thank Bharathiar
University and Rashtriya Uchchatar
Shiksha Abhiyan (RUSA 2.0) - Bharathiar Cancer Theranostics Research Centre, Coimbatore, Tamil Nadu, India
for the support.
Introduction
A herbarium is a collection of
preserved plant specimens, which are repositories to safeguard plant samples of
a given area or region and serve as reference materials to build knowledge of
biological resources. Virtual or digital herbaria are playing an important role
as a large number of plant specimens are digitized and serve as virtual museums
and as libraries of information about plants (Primack et al. 2004). A Virtual
herbarium is a digitized form of biological specimens, containing a collection
of digital images of preserved plants or plant parts which in turn is useful in
improving availability of specimens to all users. In addition, storage of more
samples in less space without using herbarium sheet, maintenance of original colour, shape and size of samples without microbial attack
and odour emission are the salient features of a
virtual herbarium (Flannery 2013). The information on botanical collections is
made accessible through digitization, database development and the internet
through Barcoding Library (BL) and Quick Response (QR) codes in the digital
era.
Barcodes are created in response
to the requirement of industries to develop a system to capture the product
data quickly during the check-out process at supermarkets. They are
one-dimensional optical representations, where widths and spacing of parallel
lines are translated primarily into numeric data (Law & So 2010). The
information in the barcodes are decoded by electronic devices, linked to a
database. There are applications available on the internet to decode the
barcode information. Similarly, QR codes are the 2-dimensional barcodes used in
the trademark for a type of matrix which has gained recognition as an effective
tool for product information. These codes connect digital resources to printed
text, suggesting the potential to enhance paper-based learning materials (Chen
et al. 2011). It can be read from any direction in 360° through position
detection located at the three corners (Moisoiu et
al. 2014).
University of Washington
Herbarium has developed a virtual database of around 72 genera of lichens. US
National Science Foundation along with North American Lichen Herbaria created a
virtual database containing 2.3 million North American lichen and bryophyte
specimens (Lai 2006). African plants initiative scheme was established in 2013
with the aim of digitizing type specimens and making these images available on
the website (Patmore 2010). The American plant systematics created a rich
website on Lewis and Clark’s botanical collections and Linnean
Society’s website exhibited plant specimens, insects, fish, and shells in
digital form (Reveal 2008). But no efforts were undertaken to create QR codes
for repository biological specimens for quick access to get the information
about repository specimens especially for lichens.
A digital herbarium is useful to
improve the access of potential application and diversity of the lichens which
in turn is useful to maintain lichen resources in India. In addition, lichens
are slow growers and require several years to develop thallus to the length of
1 cm (Ahmadjian 1993). Keeping this in mind, studies
were undertaken to create a virtual herbarium for lichens using digital
picturization, barcoding and QR code techniques in cloud environment. A simple
and rapid protocol was standardized to create virtual herbarium for lichens and
subsequently made available online for Lichenologists.
Materials
and Methods
Collection and identification of
lichen samples
Lichen samples were collected
from various living and non-living substrates in the Eastern Ghats (Kolli & Yercaud hills) and
the Western Ghats (Kodaikanal & Nilgiris hills) of Tamil Nadu, India and were identified by
following the standard method of Awasthi (2007). Lichen morphology, anatomy,
growth forms, powdery appearance and nature of fruiting bodies embedded on the
thallus were critically analysed to identify the
lichen communities from genus to species level. Chemical tests (K, C, KC, and
PD) were employed to observe the colour reactions on
lichen thallus including the existence of lichen secondary metabolites. Lichen
thallus were examined for the cortical and medullary chemical compounds by thin
layer chromatography method using a suitable solvent system (Orange et al.
2001). The specimens were deposited in the Department of Botany, Bharathiar University, Coimbatore, Tamil Nadu, India as per
the conventional method.
Digitization and preparation of
Barcoding for lichen specimens
The collected lichen thalli were
placed in an Image capturing documentation system fitted with a high resolution
digital camera (Precision Co, Ltd, India) to capture the overall images of
lichens without any background noise error to minimise
the pixel size. Lichen images were also directly photographed using high
resolution digital cameras or smartphones with different dimensions on the
substratum without disturbing the lichen biodiversity. Lichen images were taken
to observe specific parts such as
isidia, rhizines, apothesia,
soredia etc to understand the digitalized herbarium (https://www.digitallichenbu.in/).
Selected images of lichens with
smaller pixel size were transferred to a computer terminal installed with a
barcode generator software studio containing RFID label software (TBarCode SDK Activator@) to generate barcodes (Ginni et al. 2022). The barcoding data was generated with
individual bars along with numeric numbers without any decimal for lichen
specimens such as Chrysothrix candelaris (L.) J.R.Laundon
(BU/BRL/2022/002), Leucodermia leucomelos
(L.) Kalb (BU/BRL/2022/022), Heterodernia
flabellate (fee) D.D.Awasthi BU/BRL/2022/012),
Parmotrema andinum
(Mull.Arg.) Hale (BU/BRL/2022/024), Parmotrema grayanum (Hue)
Hale (BU/BRL/2022/025), Parmellinella
stuppeum (Taylor) Hale (BU/BRL/2022/031), and
Ramalina intermedia (Delise ex Nyl.) Nyl. (BU/BRL/2022/036).
Digitization and preparation of
QR codes for
lichen specimens
In order to create QR codes for
each lichen specimen, QR code generator software studio containing MacOSX.pkg. 10.8+Version: 1.0.3 software was used and then
processed digitally so as to read the contents rapidly. Attempts were made to
read QR codes in both windows PC and mobile phone devices. If the mobile device
did not build in any QR code reader, the user needs to download the right
decoder from google play store and install it on to the device. The generated
image files as QR codes were used to identify the lichen specimens from genus
to species level along with detailed descriptions such as distribution, habit
and habitat, family, nature of thallus, reproductive structure, chemistry (colour tests) and secondary metabolites of each lichen
sample and were documented (Diazgranados & Funk
2013).
Results
Barcodes and QR codes empowered
virtual herbarium for lichens was created wherein, the virtual data was made
available online. The virtual data such as digital image, name, and
descriptions of lichens were presented. Digital picturization as virtual data
for lichen identification can be accessed by the end users of both Windows PCs
and smartphone mobile devices online using both barcode and QR code techniques.
The end users need to download the right decoder software from google play
store and install it on to the device for QR codes. On the other hand, a
barcode scanner is necessary to scan the barcode to read the data. The barcodes
were generated and displayed in the conventional lichen herbarium in Bharathiar University, Coimbatore, India to get the details
of particular lichen specimens. If we scan the barcodes, the binomial name of
lichen specimens and their accession numbers are displayed.
Lichen specimens such as Chrysothrix candelaris (L.)
J.R.Laundon, belonging to crustose, Leucodermia leucomelos (L.)
Kalb, Heterodernia flabellate (fee) D.D.Awasthi, Parmotrema andinum (Mull.Arg.) Hale, Parmotrema grayanum (Hue)
Hale, Parmellinella stuppeum
(Taylor) Hale belonging to foliose and Ramalina
intermedia (Delise ex Nyl.)
Nyl. belonging to fruticose growth forms were
identified from genus to species level (Image 1). Different genus and groups of
the lichens name was given different code to predict the digital herbarium
sample. These repository specimens have been deposited in the lichen herbarium
as reference materials as per the conventional method of preparation for future
taxonomic studies (Image 2). By using the barcode generator software studio,
barcodes were generated and labelled properly for each repository specimen
along with their accession numbers (Table 1).
According to Table 2, QR codes
were created for all of the chosen lichen species and they provide a brief
description that includes information on distribution, habit & habitat,
growth forms, name of the family, reproductive structure, chemistry (colour tests), nature of thallus structure, and existence
of secondary metabolites. Along with detailed descriptions of each lichen
specimen, a digital image is also displayed on the screen. A simple, reliable
with reproducible protocol was developed to identify the repository specimens
using QR code reader significantly (Image 3). Barcode and QR approaches reveal
easy identification and prediction of lichen images very fast with a complete
description.
Discussion
Lichenologists identify lichen
species routinely by their external and internal morphology along with chemical
constituents contained in thallus and to some extent to molecular traits by
means of DNA profile (Upreti et al. 2005). Lichen
taxonomy is a very complex and time-consuming process that also suffers from
shortage of skilled manpower (Nayaka & Upreti
2013). A large number of lichens are being preserved using conventional
herbarium methods for a variety of research and teaching and learning purposes
in the world. But to the best of our knowledge, no attempt has been made so far
for developing a virtual herbarium for lichens using digital picturization,
barcoding library and QR code techniques in India. The present study was
developed to establish a virtual herbarium for lichens with a simple, reliable
and user-friendly protocol (Image 3). For a few specimens a barcode library and
QR code information virtual data were developed and made available on the
website https://www.digitallichenbu.in/
(Tables 1 & 2).
Both barcodes and QR codes showed
brief information about the lichen characteristic features in a
machine-readable optical label structure. It is used extensively in research
for barcoding of flora and fauna in the digital world. Each barcode image is
programmed to identify the name of the plant and other information relevant to
the plant family, order and taxonomical description. A large number of benefits
of QR codes and barcoding system have been listed out (Chase & Fay 2009)
like improved inventory management, faster check-in and check-out facility,
easy to sort out the specimens, reduced staff workload and skilled man power
and increased accuracy and efficiency (Singh 2016).
Virtual herbarium of angio-spermic plants of the Western Ghats of Maharashtra, India, is
available with the Modern College of Arts, Science and Commerce, Pune,
Maharashtra, India, in which a list of about 1,000 species was made, of which
650 plants were documented and the data on 350 plants is currently available on
the website (Singh & Sharma 2009). The primary objective of this project
was to capture and store high quality digital images of plant species and to
make this database available to students, researchers, and public to
disseminate the awareness of regional plants (http://www.indianflora.org/). A
virtual herbarium for the higher plants has been created at the Kerala Forest
Research Institute, Peechi, Kerala, India, which
provides a total of 5,718 records representing 203 plant families and is
rendered accessible at http://kfriherbarium.org/ (Sreekumar et al. 2017).
Similarly, a digital herbarium for the flora of Karnataka was carried out by
Rao et al. (2012) at the Indian Institute of Science, Bangalore, India.
The high-resolution images of
digitized plant specimens through virtual herbarium techniques may be useful to
examine micro-morphological features of plant parts and can further access the
repository specimen information recorded on the data sheet. In addition, using
barcodes, plant specimens could be sorted out based on family and order as per
the classification with more accuracy and efficiency in the virtual herbarium
(Dmitry et al. 2017). It is reported that virtual lichen herbarium is less
time-consuming and needs fewer skilled manpower; also explores the bioactive
properties of lichen genera for industrial applications (Flannery 2013). A
digital lichen herbarium might be useful to researchers to easily access the
lichens of the specific herbaria for their studies.
To conclude, lichen specimens
such as Chrysothrix candelaris
(L.) J.R.Laundon, Leucodermia leucomelos (L.) Kalb, Heterodernia
flabellate (fee) D.D.Awasthi, Parmotrema andinum (Mull.Arg.) Hale, Parmotrema grayanum (Hue) Hale, Parmellinella
stuppeum (Taylor) Hale, and Ramalina intermedia (Delise
ex Nyl.) Nyl. collected
from the Eastern Ghats and the Western
Ghats of Tamil Nadu, India were digitalized for making a virtual herbarium. The
barcodes and quick response (QR) codes were used in the virtual lichen
herbarium for quick access and to get a complete description of the repository
specimens based on morphological, anatomical and biochemical characterization
traits. The present attempt may be highly useful to lichenologists and
biodiversity conservation scientists to get information about lichens in digital
form without disturbing the lichen biodiversity in the habitats.
Table 1. Barcoding for lichen specimens and the
accession number.
|
|
Barcode |
Binomial
name |
Accession
number |
|
1.
|
|
Chrysothrix candelaris (L.) J.R. Laundon |
BU/BRL/2022/002 |
|
2.
|
|
Leucodermia leucomelos (L.) Kalb |
BU/BRL/2022/022 |
|
3.
|
|
Heterodernia flabellate (fee) D.D.Awasthi |
BU/BRL/2022/012 |
|
4.
|
|
Parmotrema andinum (Mull.Arg.) Hale |
BU/BRL/2022/024 |
|
5.
|
|
Parmotrema grayanum
(Hue)Hale |
BU/BRL/2022/025 |
|
6.
|
|
Parmellinella stuppeum (Taylor)
Hale |
BU/BRL/2022/031 |
|
7. |
|
Ramalina intermedia (Delise ex Nyl.) Nyl |
BU/BRL/2022/036 |
