Scientists are utilizing environmental DNA (eDNA) shed by living organisms to study biodiversity. EU-funded LeDNA project collects eDNA from lakes to assess and discover species, aiding global biodiversity preservation efforts. On World Biodiversity Day, May 22, 2024, a citizen science survey will test the method’s scalability, involving people worldwide in lake eDNA sampling using a specially designed device. Similarly, the BIOSPACE project explores eDNA in forests, predicting microbial biodiversity with satellite imagery, offering systematic and unbiased insights into lesser-known species for comprehensive biodiversity conservation.
Cottonwood trees are crucial for biodiversity in the arid Southwest, but less than 3% of their pre-20th-century distribution remains. A new study reveals their genetics influence insect and fungal communities. To preserve these ecosystems, reforestation efforts should consider tree genetics and collect seeds from nearby regions with resilient traits. Planting diverse trees supports diverse communities, ensuring the survival of this vital foundation species.
Anthropogenic climate change has, together with the intensive use and destruction of natural ecosystems through agriculture, fishing and industry, sparked an unprecedented loss of biodiversity that continues to worsen. In this regard, the climate crisis and biodiversity crisis are often viewed as two separate catastrophes. An international team of researchers calls for adopting a new perspective. In their review study they recommend (in addition to complying with the 1.5-degree target) protecting and restoring at least 30 percent of all land, freshwater and marine zones, establishing a network of interconnected protected areas, and promoting interdisciplinary collaboration between political institutions, which often operate independently.
A report by Dr. Deena Errampalli, Head of the Global Plant Council Delegation at the COP15 (7-19 December 2022 in Montreal, Canada)
Do you know that 60% of terrestrial wildlife, including plant, animal, insect, and fungal species, has been lost in the last 50 years? Similar biodiversity loss is occurring in Marine wildlife, as well. A recent UN Report warns that the current rate of species extinction is at historic levels and is “accelerating.”
There is every reason to be concerned as if we do not take action, the loss of biodiversity will jeopardize food and water supplies and cause ecosystem collapse. Only by working together at the global level can we prevent biodiversity loss.
What is COP 15?
COP 15 was the 15th meeting of the Conference of the Parties (COP15) to the United Nations Convention on Biological Diversity (CBD) that brought together over 12,000 delegates from 188 countries to engage in important negotiations and dialogue around global biodiversity conservation. The parties in COP refer to the countries. COP15 met from 7 -19 December 2022 in Montreal, Canada.
My name is Deena Errampalli; Research Scientist (plant pathology) in Canada and a board member at the Global Plant Council (GPC), and was delighted to lead the in-person GPC delegation, in an Observer capacity, in Montreal. Scientists from different delegations including DSI Scientific Network and the Global Plant Council, advocated for a post-2020 Global Biodiversity Framework by making science-based presentations at the side events and consulting with different parties at the convention.
My first steps at COP15
After registering and obtaining a badge, and then immediately doing a COVID rapid test (a daily negative test was required for entrance to the venue), I made it to the COP15 Opening Ceremony and heard inspiring opening remarks from dignitaries. Canada’s Prime Minister, Justin Trudeau’s welcomed the COP15 delegates to Canada with a speech and a funding announcement for a biodiversity saving initiative. Next, the UN Secretary-General António Guterres welcomed the delegates, followed by Minister Huang Runqiu, President of the Fifteenth Meeting of the Conference of the Parties to the United Nations Convention on Biological Diversity (COP 15) and Minister of Ecology and Environment of China in Chinese. Both Francois Legaults, the Premier of Quebec Province, and Valérie Plante, the Mayor of Montreal spoke in French. Of course, there were simultaneous translations to many languages were available at the convention.
The UN secretary general, António Guterres, opened the Convention with a stark message: “Without nature, we are nothing. Nature is our life-support system, and yet humanity seems hellbent on destruction.” He added, “With our bottomless appetite for unchecked and unequal economic growth, humanity has become a weapon of mass extinction,” he said. “[COP15] is our chance to stop this orgy of destruction, to move from discord to harmony.”
The primary aim of COP15 was to ‘give-teeth’ to the Convention on Biological Diversity adopted at Earth Summit in Aichi, Brazil, in 1992, and ratified by 196 countries, albeit with the notable exception of the USA.
Countries from around the world came together at COP15 to agree on a new set of goals to guide global action through 2030 to halt and reverse nature loss and to protect 30 percent of the planet’s land and oceans. It is also known as ‘30 X 30’.
On genetic sources
One of the issues that GPC advocated was the Digital Sequence Information (DSI) on genetic sources. As Parties (countries) to the Convention on Biological Diversity debated the issue of access and benefit-sharing from DSI on genetic sources at the COP15 UN Biodiversity Conference, a group of scientists has proposed a multilateral framework where access to DSI from genetic resources is “decoupled” from benefit sharing. On invitation, I presented a case study titled, “How DSI can revolutionize food security: understanding the Sterility Mosaic Disease of Pigeonpea“, at the “A comparative analysis of policy options for DSI under the CBD: how do they measure up?” a side event organized by the DSI Scientific Network at COP15 on 8 December, 2022.
I (from Canada) was invited as a panelist along with Manuela da Silva, Fiocruz (Brazil), Amber Scholz, DSMZ Leibniz (Germany), Guilherme Oliveira, Instituto Tecnologico Vale (ITV; Brazil), and two moderators, Christian Tiambo, Centre for Tropical Livestock Genetic and Health (CTLGH) – International Livestock Research Institute (ILRI; South Africa) and Jens Freitag, Leibniz Institute of Plant Genomics and Crop Plant Research (IPK; Germany). The DSI side event was well-attended and well-received. The panel answered/clarified some of the questions from the audience, which included ‘Parties.’
In the early hours (3:30 am to be precise) of December 19, 2022, after years of negotiations, including two weeks of intense negotiations in Montreal, the delegates from 188 countries finally reached a deal to share benefits from the use of digital sequence information (DSI) derived from genetic resources. COP15 ended with a landmark biodiversity agreement, where nations adopted four goals, 23 targets for 2030.
To put it in perspective, the GBF agreement for nature in Montreal is equivalent to the Paris agreement for Environment. In Paris, the world agreed to an apex target to limit global warming to well below +2C, preferably to +1.5˚C, and with the 2022 GBF the world had agreed to ‘30 x 30’ target.
Despite the hesitations of some, the Convention on Biological Diversity text pledging open access to gene-sequence information was a relief to the scientific research community, which had voiced worries about losing access to genetic sequence libraries. For further details on Global Biodiversity Framework please check the official press release and PDF.
“In Montréal, we have risen to the challenge and united as one global community to address the crisis faced by nature. We agreed on an ambitious path forward for our planet, and have given ourselves the tools to turn the tide. This is a historic moment for nature, and it is our only chance to save what we love and hold dear, before it is too late.”– The Honourable Steven Guilbeault, Minister of Environment and Climate Change Canada.
The delegates and all the concerned communities worldwide rejoiced to have reached the Global Biodiversity Framework agreement in 2022, and the next steps, the real work begins in implementing it.
Attending COP 15 and being a part of the convention that saw the GBF agreement approved was a career highlight for me. It was an incredible experience to hear the passionate, at times contradicting, views of so many delegates from across the globe ranging from small island nations such as Fiji to large land-based countries like Canada. A total of 188 countries were present.
The knowledge that all of us were working towards a common goal of protecting the biodiversity of our planet was both exhilarating and humbling. This new “Global Biodiversity Framework” of 2022 has set out targets for the coming decade to 2030. These targets will replace the Aichi targets set for 2011-2020 and will also lead towards the longer 2050 goal: living in harmony with nature.
With the 2022 GBF agreement, I am feeling hopeful and excited for all flora and fauna on this earth. This GBF matters for the future of our food and agriculture. I hope that the nations will follow through with the agreement to protect global biodiversity and realize the dream of a Healthy Planet and Healthy People.
About the author: Dr. Deena Errampalli is a scientist (Plant Pathologist) in agriculture. She is also a Board member of the Global Plant Council, a not-for-profit Corporation based in Canada. Download her report here.
About The Global Plant Council: an umbrella organization of plant, crop, agricultural, and environmental science societies and organizations across the globe representing thousands of experts. In the past few years, the GPC has provided a platform for debate on open access to digital gene-sequence information.
As forests age, differences in species functional traits become more important and reliable in predicting forest productivity, according to an international study.
An international team of researchers has identified genes associated with plant survival in one of the harshest environments on Earth: the Atacama Desert in Chile.
It is commonly assumed that any important scientific knowledge would be available in English, and so scientific knowledge used in international studies is predominantly sourced from English-language documents. But is this assumption correct? According to new research the answer is no, and science written in languages other than English may hold untapped information crucial to the conservation of global biodiversity.
The 1000 plants initiative (1KP) is a multidisciplinary consortium aiming to generate large-scale gene sequencing data for over 1000 species of plants. Included in these species are those of interest to agriculture and medicines, as well as green algae, extremophytes and non-flowering plants. The project is funded by several supporters, and has already generated many published papers.
Gane Wong is a Professor in the Faculty of Science at the University of Alberta in Canada. Having previously worked on the Human Genome Project, he now leads the 1KP initiative. Dennis Stevenson, Vice President for Botanical Research, New York Botanical Garden, and Adjunct Professor, Cornell University (USA), studies the evolution and classification of the Cycadales. He became involved in the 1KP initiative as an opportunity to sample the breadth of green plant diversity.
We spoke to both Professor Stevenson (DS) and Professor Wong (GW) about the initiative. Professor Douglas Soltis from Florida Museum of Natural History also contributed to this blog post with input in editing the answers.
What do you think has been the biggest benefit of 1KP?
DS: This has been an unparalleled opportunity to reveal and understand the genes that have led to the plant diversity we see around us. We were able to study plants that were pivotal in terms of plant evolution but which have not previously been included in sequencing projects as they are not considered important economically
GW: The project was funded by the Government of Alberta and the investment firm Musea Ventures to raise the profile of the University of Alberta. Notably there was no requirement by the funders to sequence any particular species. I was able to ask the plant science community what the best possible use of these resources would be. The community was in full agreement that the money should be used to sample plant diversity.
Hopefully our work will change the thinking at the funding agencies regarding the value of sequencing biodiversity.
What techniques were utilized in this project to carry out the research?
GW: Complete genomes were too expensive to sequence. Many plants have unusually large genomes and de novo assembly of a polyploid genome remains difficult. To overcome this problem, we sequenced transcriptomes. However, this made our sample collection more difficult as the tissue had to be fresh. In addition, when we started the project, the software to assemble de novo transcriptomes did not work particularly well. I simply made a bet that these problems would be solved by the time we collected the samples and extracted the RNA. For the most part that’s what happened, although we did end up developing our own assembly software as well!
The 1KP initiative is an international consortium. How has the group evolved over time and what benefits have you seen from having this diverse set of skills?
GW: 1KP would not be where it is today without the participation of scientists around the world from many different backgrounds. For example, plant systematists who defined species of interest and provided the tissue samples worked alongside bioinformaticians who analyzed the data, and gene family experts who are now publishing fascinating stories about particular genes.
DS: One of the great things about this project is how it has evolved over time as new researchers became involved. There is no restriction on who can take part, which species can be studied or which questions can be asked of the data. This makes the 1KP initiative unique compared to more traditionally funded projects.
GW: We continually encouraged others to get involved and mine our data for interesting information. We did a lot of this through word of mouth and ended up with some highly interesting, unexpected discoveries. For example, an optogenetics group at MIT and Harvard used our data to develop new tools for mammalian neurosciences. This really highlights the importance of not restricting the species we study to those of known economic importance.
You aimed to investigate a highly diverse array of plants. How many plants of the major phylogenetic groups have now been sequenced, and are you still working on expanding the data set?
DS: A lot of thought went into the species selection. We aimed for proportional representation (by number of species) of the major plant groups. We also aimed to represent the morphological diversity of those groups.
GW: Altogether, we generated 1345 transcriptomes from 1174 plant species.
Has this project lead to any breakthroughs in our understanding of the phylogeny of plants?
DS: This will be the first broad look at what the nuclear genome has to tell us, and the first meaningful comparison of large nuclear and plastid data sets. However, due to rapid evolution plus extinction, many parts of the plant evolutionary tree remain extremely difficult to solve.
One significant breakthrough was the discovery of horizontal gene transfer from a hornwort to a group of ferns. This was unexpected and very interesting in terms of the ability of those ferns to be able to accommodate understory habitats.
GW: With regard to horizontal gene transfer, there are papers in the pipeline that will illustrate the discovery of even more of these events in other species. We have also studied gene duplications at the whole genome and gene family level. This is the most comprehensive survey ever undertaken, and people will be surprised at the scale of the discoveries. However, we will be releasing our findings shortly as part of a series and it would be unwise for us to give the story away here! Keep a look out for these!
With another year nearly over we recently put out a call for nominations for the Most Influential Plant Science Research of 2015. Suggestions flooded in, and we also trawled through our social media feeds to see which stories inspired the most discussion and engagement. It was fantastic to read about so much amazing research from around the world. Below are our top five, selected based on impact for the plant science research community, engagement on social media, and importance for both policy and potential end product/application.
Choosing the most inspiring stories was not an easy job. If you think we’ve missed something, please let us know in the comments below, or via Twitter! In the coming weeks we’ll be posting a 2015 Plant Science Round Up, which will include other exciting research that didn’t quite make the top five, so watch this space!
- Sweet potato is a naturally occurring GM crop
Scientists at the International Potato Center in Lima, Peru, found that 291 varieties of sweet potato actually contain bacterial genes. This technically means that sweet potato is a naturally occurring genetically modified crop! Alongside all the general discussion about GM regulations, particularly in parts of Europe where regulations about growing GM crops have been decentralized from Brussels to individual EU Member States, this story caused much discussion on social media when it was published in March of this year.
It is thought that ancestors of the modern sweet potato were genetically modified by bacteria in the soil some 8000 years ago. Scientists hypothesize that it was this modification that made consumption and domestication of the crop possible. Unlike the potato, sweet potato is not a tuber but a mere root. The bacteria genes are thought to be responsible for root swelling, giving it the fleshy appearance we recognize today.
This story is incredibly important, firstly because sweet potato is the world’s seventh most important food crop, so knowledge of its genetics and development are essential for future food supply. Secondly, Agrobacterium is frequently used by scientists to artificially genetically modify plants. Evidence that this process occurs in nature opens up the conversation about GM, the methods used in this technology, and the safety of these products for human consumption.
Read the original paper in PNAS here.
- RNA-guided Cas9 nuclease creates targetable heritable mutations in Barley and Brassica
Our number two on the list also relates to genetic modification, this time focusing on methods. Regardless of whether or not we want to have genetically modified crops in our food supply, GM is a valuable tool used by researchers to advance knowledge of gene function at the genetic and phenotypic level. Therefore, systems of modification that make the process faster, cheaper, and more accurate provide fantastic opportunities for the plant science community to progress its understanding.
The Cas9 system is a method of genome editing that can make precise changes at specific locations in the genome relatively cheaply. This novel system uses small non-coding RNA to direct Cas9 nuclease to the DNA target site. This type of RNA is small and easy to program, providing a flexible and easily accessible system for genome editing.
Inheritance of genome modifications using Cas9 has previously been shown in the model plants, Arabidopsis and rice. However, the efficiency of this inheritance, and therefore potential application in crop plants has been questionable.
The breakthrough study published in November by researchers at The Sainsbury Laboratory and John Innes Centre both in Norwich, UK, demonstrated the mutation of two commercial crop plants, Barley and Brassica oleracea, using the Cas9 system and subsequent inheritance mutations.
This is an incredibly exciting development in the plant sciences and opens up many options in the future in terms of genome editing and plant science research.
Read the full paper in Genome Biology here.
- Control of Striga growth
Striga is a parasitic plant that mainly affects parts of Africa. It is a major threat to food crops such as rice and corn, leading to yield losses worth over 10 billion US dollars, and affecting over 100 million people.
Striga infects the host crop plant through its roots, depriving them of their nutrients and water. The plant hormone strigolactone, which is released by host plants, is known to induce Striga germination when host plants are nearby.
In a study published in August of this year the Striga receptors for this hormone, and the proteins responsible for striga germination were identified.
Striga plants are known to wither and die if they cannot find a host plant upon germination. Induction of early germination using synthetic hormones could therefore remove Striga populations before crops are planted. This work is vital in terms of regulating Striga populations in areas where they are hugely damaging to crop plants and people’s livelihoods.
Read the full study in Science here.
- Resurrection plants genome harvesting
Resurrection plants are a unique group of flora that can survive extreme water shortages for months or even years. There are more than 130 varieties in the world, and many researchers believe that unlocking the genetic codes of drought-tolerant plants could help farmers working in increasingly hot and dry conditions.
During a drought, the plant acts like a seed, becoming so dry that it appears dead. But as soon as the rains come, the shriveled plant bursts ‘back to life’, turning green and robust in just a few hours.
In November, researchers from the Donald Danforth Plant Science Centre in Missouri, US, published the complete draft genome of Oropetium thomaeum, a resurrection grass species.
O. thomaeum is a small C4 grass species found in Africa and India. It is closely related to major food feed and bioenergy crops. Therefore this work represents a significant step in terms of understanding novel drought tolerance mechanisms that could be used in agriculture.
Read the full paper in Nature here.
- Supercomputing overcomes major ecological challenge
Currently, one of the greatest challenges for ecologists is to quantify plant diversity and understand how this affects plant survival. For the last 500 years independent research groups around the world have collected this diversity data, which has made organization and collaboration difficult in the past.
Over the last 500 years, independent research groups have collected a wealth of diversity data. The Botanical Information and Ecology Network (BIEN) are collecting and collating these data together for the Americas using high performance computing (HPC) and data resources, via the iPlant Collaborative and the Texas Advanced Computing Center (TACC). This will allow researchers to draw on data right from the earliest plant collections up to the modern day to understand plant diversity.
There are approximately 120,000 plant species in North and South America, but mapping and determining the hotspots of species richness requires computationally intensive geographic range estimates. With supercomputing the BIEN group could generate and store geographic range estimates for plant species in the Americas.
It also gives ecologists the ability to document continental scale patterns of species diversity, which show where any species of plant might be found. These novel maps could prove a fantastic resource for ecologists working on diversity and conservation.
Read more about this story on the TACC website, here.