2023 Archives - Botany Boost Blog

Bio sequestration: Harnessing Plant Life to Mitigate Climate Change

by Kosala AbeykoonJanuary 8, 2024January 13, 20242023 / Plant biotechnologyLeave a Comment

Climatic change is a significant concern for the future of our planet, and one potential solution to mitigate its effects is plant-based carbon sequestration. This article will discuss the role of plants in carbon sequestration and how they can contribute to reducing atmospheric greenhouse gas levels. The fundamental process of carbon sequestration in plants begins with photosynthesis, a complex biochemical mechanism that goes beyond just absorbing carbon. Photosynthetic organisms, primarily plants, utilize solar energy to convert atmospheric carbon dioxide (CO2) into organic compounds, releasing oxygen as a byproduct. In recent years, researchers have delved deeper into understanding the intricate molecular processes involved in photosynthesis, aiming to enhance the efficiency of carbon fixation and storage.

Advancements in plant genomics have paved the way for the identification and manipulation of key genes responsible for photosynthetic performance. Genetic engineering techniques, such as CRISPR-Cas9, offer the potential to create crops with increased photosynthetic rates and improved carbon sequestration capabilities. This targeted approach aligns with the broader goal of developing climate-resilient and high-yielding plant varieties that can contribute significantly to minimize atmospheric carbon levels.

Figure 1: A schematic showing carbon sequestration

Effectiveness of Different Ecosystems for Plant-Based Carbon Sequestration

The effectiveness of plant-based carbon sequestration varies across different ecosystems, each presenting unique opportunities and challenges. Understanding how diverse ecosystems contribute to carbon sequestration is crucial for developing targeted strategies that optimize their potential.
Blue carbon refers to the carbon captured and stored by the world’s ocean and coastal ecosystems, such as mangroves, seagrass meadows, and tidal marshes (Figure 2). These ecosystems play a crucial role in climate change mitigation and adaptation, as they sequester and store carbon at a faster rate than terrestrial forests.

1. Forests and Woodlands:
Forests are among the most effective ecosystems for carbon sequestration due to the large biomass of trees and the long-term storage potential in woody tissues. Old-growth forests, in particular, play a vital role in sequestering carbon over extended periods. However, careful consideration is required to balance the carbon sequestration benefits with biodiversity conservation, as monoculture plantations may not provide the same ecological services as diverse natural forests.

2. Grasslands and Wetlands:
Grasslands and wetlands, while often overlooked, contribute significantly to carbon sequestration. Grasses capture carbon in their roots and soil, and wetlands act as carbon sinks due to the anaerobic conditions that slow down the decomposition of organic matter. Sustainable management of these ecosystems, including rotational grazing and wetland restoration, enhances their carbon sequestration potential.

3. Mangroves and Coastal Ecosystems:
Mangroves and coastal ecosystems are highly effective at sequestering carbon, both in above-ground biomass and in the sediment below. The unique conditions in these areas, characterized by saline water and waterlogged soils, create an environment where organic matter decomposes slowly. Conservation and restoration of mangroves not only contribute to carbon sequestration but also provide critical habitat for marine life and act as buffers against coastal erosion.

4. Agricultural Lands:
Agricultural lands, when managed sustainably, can contribute to carbon sequestration through practices such as cover cropping, agroforestry, and no-till farming. These approaches enhance soil organic carbon content, improving soil structure and fertility. Precision agriculture technologies further optimize the efficiency of these practices, ensuring that agricultural lands become part of the solution to climate change.

5. Urban Green Spaces:
Urban green spaces, including parks and green belts, play a role in carbon sequestration within urban environments. While the contribution may be smaller compared to larger ecosystems, the collective impact of strategically placed green spaces can help mitigate the urban heat island effect and enhance local air quality. Incorporating trees and vegetation into urban planning fosters a balance between carbon sequestration and human well-being.

6. Alpine Ecosystems:
Alpine ecosystems, characterized by high-altitude regions, contribute to carbon sequestration through the slow decomposition of organic matter in cold and oxygen-deprived conditions. As temperatures rise due to climate change, there is concern about the potential release of stored carbon from these ecosystems. Sustainable conservation practices are essential to maintain the effectiveness of alpine ecosystems in sequestering carbon.

Figure 2: Blue Carbon

Integrating Ecosystems for Synergistic Carbon Sequestration

Recognizing the diverse contributions of different ecosystems, an integrated approach that combines afforestation, reforestation, and sustainable land management practices is paramount. Synergies between ecosystems can amplify overall carbon sequestration benefits. For example, agroforestry practices that integrate trees into agricultural landscapes not only sequester carbon in biomass but also enhance soil carbon levels.

Furthermore, the preservation of natural ecosystems and the restoration of degraded areas contribute to maintaining biodiversity, ecosystem resilience, and the overall health of the planet. Climate-adaptive strategies, as discussed earlier, should consider the specific characteristics of different ecosystems and tailor interventions accordingly.

The effectiveness of plant-based carbon sequestration is intricately linked to the diverse ecosystems that cover our planet. By understanding and harnessing the unique strengths of each ecosystem, we can develop comprehensive strategies that maximize the potential of plant-based carbon sequestration, contributing to a more sustainable and resilient future.

Advanced Techniques in Plant-Based Carbon Sequestration

1. Enhanced Afforestation and Reforestation Strategies

While afforestation and reforestation are established methods for carbon sequestration, ongoing research is focused on enhancing their efficacy. Novel approaches include the identification and cultivation of tree species with accelerated growth rates and high carbon sequestration potential. Genetic modification techniques are explored to develop trees with increased biomass and improved resistance to environmental stressors, thereby maximizing carbon absorption and storage.

Additionally, precision forestry, aided by satellite imaging and machine learning algorithms, allows for optimal placement of trees based on soil conditions, climate patterns, and local ecological factors. This strategic placement not only enhances carbon sequestration efficiency but also minimizes potential negative impacts on local biodiversity.

2. Advanced Bioenergy with Carbon Capture and Storage (BECCS)

Continued advancements in BECCS technology are crucial for its integration into comprehensive carbon sequestration strategies. Research is underway to improve the efficiency of CO2 capture methods and explore alternative storage solutions, such as utilizing captured carbon for the synthesis of valuable products or converting it into stable mineral forms. These innovations aim to address the economic feasibility and sustainability concerns associated with BECCS.

Furthermore, the exploration of alternative biomass feedstocks, such as algae and fast-growing perennial grasses, is underway to enhance the carbon capture potential of bioenergy systems. Integrating these feedstocks with traditional afforestation and reforestation practices creates a synergistic effect, amplifying the overall carbon sequestration capacity.

3. Precision Soil Carbon Sequestration Practices

Advancements in agricultural practices are crucial for optimizing soil carbon sequestration. Precision agriculture, facilitated by technologies like remote sensing and data analytics, enables farmers to tailor their approaches based on specific soil characteristics and environmental conditions. This approach includes the utilization of cover crops that not only enhance carbon sequestration but also contribute to improved soil fertility and water retention.

In addition, the incorporation of mycorrhizal fungi into agricultural ecosystems shows promise in boosting plant nutrient uptake and, consequently, increasing biomass and carbon sequestration. Research is ongoing to understand the symbiotic relationships between plants and fungi, with the aim of developing customized microbial solutions for different crops and soil types.

Figure 3: Soil Carbon Sequestration

Addressing Challenges and Expanding Opportunities

1. Sustainable Land Management and Conservation

To address the challenge of requiring large land areas for plant-based carbon sequestration, sustainable land management practices are imperative. This involves identifying marginal lands unsuitable for conventional agriculture and utilizing them for afforestation, reforestation, or bioenergy crop cultivation. Additionally, integrating carbon sequestration initiatives with conservation efforts can help preserve biodiversity by creating corridors for wildlife movement within these managed landscapes.

2. Long-Term Monitoring and Adaptive Management

Ensuring the long-term effectiveness of plant-based carbon sequestration methods necessitates robust monitoring systems. Advances in remote sensing technologies, coupled with on-the-ground sensor networks, enable continuous tracking of carbon stocks in forests and soils. This data-driven approach allows for adaptive management strategies, where interventions can be adjusted in real-time based on changing environmental conditions and the effectiveness of implemented measures.

3. Climate-Adaptive Strategies

Recognizing the influence of climate, soil type, and local policy on the effectiveness of carbon sequestration methods, researchers are developing climate-adaptive strategies. These involve tailoring plant-based carbon sequestration approaches to specific climatic zones and soil conditions, optimizing their performance in varying environmental contexts.

Figure 4: Problems related to BECCS

Conclusion

The potential of plant-based carbon sequestration methods to mitigate climatic change is vast, and ongoing scientific advancements are expanding their capabilities. Enhanced afforestation and reforestation strategies, advanced BECCS technologies, precision soil carbon sequestration practices, and sustainable land management approaches are crucial components of a comprehensive solution. By addressing challenges and leveraging emerging opportunities, plant-based carbon sequestration can play a pivotal role in combating the escalating threat of climatic change, contributing to a more sustainable and resilient future for our planet. Continued interdisciplinary research and international collaboration are essential to fully unlock the potential of these innovative approaches.
Kosala Abeykoon
3rd Year

References :
I. Tdus. (2021). Biological Carbon Sequestration. UC Davis. https://www.ucdavis.edu/climate/definitions/carbon-sequestration/biological
II. Soil-based carbon sequestration. (n.d.). MIT Climate Portal. https://climate.mit.edu/explainers/soil-based-carbon-sequestration
III. Lorditch, E. (2022). Capturing carbon with crops, trees and Bioenergy. MSUToday. https://msutoday.msu.edu/news/2022/capturing-carbon-with-crops-trees-and-biomass
IV. Thomas, S. T., Shin, Y., La Clair, J. J., & Noel, J. P. (2021). Plant-based CO2 drawdown and storage as SiC. RSC Advances, 11(26), 15512–15518. https://doi.org/10.1039/d1ra00954k
V. Kell, D. B. (2012). Large-scale sequestration of atmospheric carbon via plant roots in natural and agricultural ecosystems: why and how. Philosophical Transactions of the Royal Society B, 367(1595), 1589–1597. https://doi.org/10.1098/rstb.2011.0244

Image Courtesies:

Featured Image: https://calrecycle.ca.gov/wp-content/uploads/sites/39/2022/02/biosequest.png?w=827
Content Image 1: https://upload.wikimedia.org/wikipedia/commons/thumb/b/b5/Carbon_sequestration-2009-10-07.svg/1024px-Carbon_sequestration-2009-10-07.svg.png
Content Image 2: https://blog.wcs.org/photo/wp-content/uploads/2021/11/blue-carbon-poster-for-WV-920×650.jpg
Content Image 3: https://ejpsoil.eu/fileadmin/projects/ejpsoil/Themes/CO2_cycle.jpg
Content Image 4 : https://www.geoengineeringmonitor.org/wp-content/uploads/2021/11/BECCS_diagram_4web.jpg

Genomics and Its Significance – I

by Savindu WeerathungaDecember 15, 2023December 15, 20232023 / Microbiology / Plant biotechnologyLeave a Comment

All biological organisms have an underlying map that governs the multitude of complex attributes, from anatomy and physiology to behavioral patterns that is characteristic to them. Therefore, understanding the map is crucial to solving many of the problems and challenges surrounding organisms. This map is what is generally referred to as the genome, i.e., the complete ensemble of DNA in a haploid set of chromosomes of an organism and the field of genomics involved in its study.

The following first part of the article is an attempt to briefly explore the field of genomics and how it has evolved throughout the years which will be followed by its significance and impact on society in the second part of the article.

Practices central to genomics

Mendel’s observations on heritable traits paved the way for the field of genetics that primarily focusses on the elements, i.e., genes, responsible for different traits characterizing a particular organism or species and their heritability from one generation to another. The field of genomics revolves around the complete genetic make-up that is the genome, therefore it describes all genes, the interactions between them and the environment. In order to achieve this, genomics have several practices central to it, which are sequencing, mapping and assembly of genomes, development of technologies to analyze the raw sequence data, and finally analyzing the data to produce useful information using databases and computational methods.

Sequencing and assembly

Rosalind Franklin’s x-ray crystallographic observations, followed by the discovery of the structure of the DNA by Watson and Crick during which they also determined DNA as a form of storage of genetic information, fortified the need to identify the exact order of deoxyribonucleotides in a given DNA sequence. Henceforth, sequencing became crucial to genomics.
Fredrick Sanger, Allan Maxam and Walter Gilbert were some of the pioneers in the development of DNA and RNA sequencing methods. However, the first generation of sequencing methods were limited to sequencing of relatively smaller nucleic acid molecules and genes.

Figure 1. Bacteriophage MS2 viewed from outside of its protein capsid

The first ever attempt at sequencing a complete genome (3569 bp) was that of the phage MS2 RNA genome in 1976. As the need for sequencing genomes of larger organisms grew, scientists, with the use of genome or DNA libraries, developed genome sequencing methods such as clone by clone method and whole genome shotgun sequencing.

Their increased automation and improved sequencing machines later saw a reduction in the time and cost of sequencing.

These sequencing technologies were complemented by methods of genome mapping, where the locations of genes were mapped based on different criteria. The first form of genetic mapping was introduced by Thomas Morgan while experimenting on the fruit fly, where he observed gene linkage and recombination. By using linkage to identify the relative positions of genes, a map of the fruit fly chromosome was created, which is referred to as the genetic linkage map. The discovery of polymorphic DNA markers allowed for the creation of genetic (linkage) maps with higher resolutions. Physical maps were another development where instead of locating the relative positions of genes, overlapping physical fragments of DNA are aligned to create a map predicting the true positions of genes.

Figure 2. Illustration of a genetic and physical map.

These developments together with improved genomic libraries paved the way for sequencing and assembly of larger genomes such as that of phage λ and Epstein-Barr virus B95-8 strain, and led to even larger genome projects including yeast genome sequencing, and the most widely known human genome project during the period of 1990 to early 2000s. Furthermore, all these sequencing and genome assembly efforts were made possible with the advent of computing technologies (efficient algorithms) in the 1980s. Some of the first genome assembling algorithms were greedy assemblers and later, assemblers based on overlap-layout-consensus, Eulerian path (based on de-Bruijn graphs) and align-layout-consensus (reference genome-based assembly) were introduced.

Processing raw sequence data

Given that enormous amounts of data were generated from sequencing efforts, scientists were now confronted with the problem of what could be done with all this raw data. The first efforts that were taken in resolving this resulted in the formation of a global database that allowed for the storage of sequence data as well as global access to it. The first ever global database to be formed was the Nucleotide Sequence Data Library by European Molecular Biology Laboratory (EMBL) which is now part of the European Nucleotide Archive (ENA). Later, it was followed by creation of the GenBank at NCBI of NIH and the DNA Data Bank of Japan (DDBJ). By joint agreement of the above 3 parties, the International Nucleotide Sequence Database Collaboration (INSDC) was formed to facilitate universal access to sequence information in all databases regardless of which database is queried. In fact, later it was made compulsory for researchers to submit any sequence data to the database ahead of publishing their results.

Concurrent developments in information technology and computer sciences in the latter part of the 20^th century provided the necessary technology for the analysis of sequence data. It eased the processing of raw sequence data, enabling the extraction and visualization of valuable data engraved in the genome of an organism. The process of extracting, identifying, and defining features associated with a genome is called genome annotation. Bioinformatics play a major role in this regard.

Information or features that is to be extracted and identified include genomic regions that do not encode for proteins, protein encoding regions and finally identifying the functions of these elements in relation to a single cell or organism. Genes are identified by the use of homology-based methods (extrinsic methods) or ab initio methods (intrinsic methods). Development of algorithms that produced alignments between sequences (global or local) provided the steppingstones to achieving this task.

Extrinsic methods resort to sequence similarity between the genomic DNA and available protein sequences, EST (Expressed Sequence Tags), cDNA, or other genomic DNA (i.e., by comparative genomics) to identify genes. Software programs like GeMoMa (Gene Model Mapper) use this method. Intrinsic methods utilize intrinsic properties characteristic to the sequence such as GC content, codon composition (codon usage bias), start and stop codons, translation initiation codon etc. Early gene predicting programs like DAGGER, GeneMark, GeneModeler used this method, whereas GENSCAN, GenomeScan, FGENESH, Twinscan like softwares utilize an integrative approach where they use both homology and ab initio methods to predict genes.

Prediction of non-coding regions such as those regions transcribing for rRNAs, tRNAs and regulatory regions, although have been predicted using sequence similarity and programs like tRNAScanSE32 (for de novo prediction of tRNAs), is still seen as a challenge since only a limited proportion of them have been identified even through experimental methods. Finally functional annotation of genes is carried out using a standard vocabulary called the Gene Ontology that was created by the joint effort of researchers of 3 databases Saccharomyces Genome Database, FlyBase, and the Mouse Genome Database. Gene ontology describes genes in terms of molecular functions, broader biological processes, and cellular components where the gene products are found or function in.

The preceding exploration certainly does not suffice in describing the efforts taken in developing the relevant technologies as well as the developments that are currently undertaken trying to decode the genomes of organisms but only peek into the world of genomics. The next part of the article will dive into the significance and impact that genomics have had on present society and its advancements.

Savindu Weerathunga

3^rd Year

References

Chaitanya, K. V. (2019). From Archaea to Eukaryotes. In Chaitanya, K. V. (Ed.). Genome and genomics. Springer Singapore. https://doi.org/10.1007/978-981-15-0702-1
García-Sancho, M., & Lowe, J. (2023). A History of Genomics across Species, Communities and Projects. Springer Nature. https://doi.org/10.1007/978-3-031-06130-1
Giani, A. M., Gallo, G. R., Gianfranceschi, L., & Formenti, G. (2020). Long walk to genomics: History and current approaches to genome sequencing and assembly. Computational and Structural Biotechnology Journal, 18, 9–19. https://doi.org/10.1016/j.csbj.2019.11.002
Mathé, C. (2002). Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Research, 30(19), 4103–4117. https://doi.org/10.1093/nar/gkf543
(2019, March 9). Genetics vs. Genomics Fact Sheet. Genome.gov. https://www.genome.gov/about-genomics/fact-sheets/Genetics-vs-Genomics

Image Courtesy

Figure 1 – https://shorturl.at/cnAV0
Figure 2 – https://shorturl.at/mBJQ2

Mitigating Climate Change Through Blue Carbon Ecosystems

by Sakalya De SilvaJuly 14, 2023July 14, 20232023 / Plant biotechnology / Plant scienceLeave a Comment

Climate change is a global crisis that is happening now. The effects of the great damage done by humans to the environment are being experienced right now by humans themselves. Warmer temperatures are changing the weather patterns, and nature’s biodiversity is in decline. Climate change is all about too much carbon in the atmosphere. However, without carbon, life would not have appeared on earth in the first place. Carbon is essential for life on earth. It is the building block of life. Every life form, including animals, plants, and even the tiniest organisms, microbes, is made up of carbon.

So, you must be wondering how, if carbon is so essential for life, the presence of excess carbon in the atmosphere becomes a threat to living organisms on earth. The greenhouse effect is a natural phenomenon occurring in the atmosphere that helps keep the planet warm. Carbon dioxide is a major gas that is responsible for this process. Hence, too much carbon in the atmosphere will accelerate the greenhouse effect by trapping more and more heat. It makes the planet warmer and warmer and eventually contributes to climate change.

If we go back to about 700 million years ago, when plants appeared on land, carbon began to cycle in an incredible balance. A balance that allowed the origin and evolution of different life forms on Earth. Plants took up carbon dioxide from the atmosphere and pumped oxygen into the atmosphere. Then, after the appearance of humans, we started to remove carbon from the soil and release it into the atmosphere by burning fossil fuels, disrupting the incredible balance created by nature. The way we cultivate plants and carry out animal husbandry releases even more carbon into the atmosphere, resulting in a global climate crisis.

So, how do we protect the life forms on earth from this global crisis? Of course, we should stop releasing carbon into the atmosphere and remove the excess carbon to get the carbon cycle back into balance. The question is, where do we put this excess carbon? We all know that plants can fix carbon in the atmosphere through photosynthesis and convert it into carbohydrates and sugars. Then these carbohydrates and sugars are pumped through the plant roots into the soil, where microorganisms can utilize them. This process is called carbon sequestration. Hence, safeguarding plants helps mitigate this global climate crisis. But recently, an even more advantageous climate mitigation opportunity has been discovered, which is to protect the blue carbon in coastal and marine ecosystems.

Fig. 1: A mangrove forest

Blue carbon is the carbon stored in marine and coastal ecosystems. These ecosystems consist of sea grass, mangrove forests, salt marshes, and phytoplankton in the oceans. Blue carbon ecosystems are considered one of the most productive ecosystems on earth. Sea grass, mangrove forests, and salt marshes are much smaller than terrestrial forests. Yet they can fix carbon at a rate of about 40 to 50 times faster than terrestrial ecosystems. Most of the carbon in these ecosystems is stored below ground and is often thousands of years old.

Fig. 2: Sea grasses

Fig. 3: Salt marshes

The oceans contain 50 times more carbon than the atmosphere. Hence, the ocean is considered the largest active carbon sink, consisting of marine plants such as seaweeds and phytoplankton. Phytoplankton are considered the primary producers of the sea. Marine organisms consume phytoplankton and seaweeds to build their bodies and skeletons. When marine life dies, the carbon stored is buried in the sea bed, locking it away in the ocean sediments.

Fig. 4: An adult sea turtle consuming sea grass leaves

In Addition to carbon sequestration, these ecosystems bring many benefits to both humans and the environment. They are considered one of the most diverse habitats on earth. They provide nursery grounds for fish, support industries like fisheries, and improve the water quality along coastlines. Moreover, blue carbon ecosystems are essential to coastal protection as they prevent coastal erosion and extreme weather events like floods, storms, tsunamis, etc.

Yet these ecosystems are severely threatened by human activities and are declining rapidly. Mangrove forest exploitation due to agriculture, coastal and marine pollution, and industrial and urban coastal development projects are some causes. Globally, mangrove deforestation occurs at a rate of 2% per year and accounts for about 10% of global greenhouse gas emissions. Blue carbon ecosystems play an essential role in storing excess carbon. But the destruction of the habitat makes them a source of greenhouse gas emissions. When deteriorated or destroyed, they emit massive amounts of carbon into the atmosphere that have been sequestered for millions of years, which is similar to a carbon bomb. Thus, these habitats play a vital role in mitigating climate change, unless they deteriorate. So we must protect and restore these ecosystems through the implementation of suitable national and international climate policies and community-led projects to attenuate the climate change issue.

Fig. 5: Deforested mangrove forest in Madagascar

The clock is ticking. There is not much time left for us. We need to act soon before the consequences of our actions become irreversible. Remember when I mentioned earlier that we need to stop releasing carbon into the atmosphere and remove the excess carbon to get the carbon cycle back into balance? Hence, we have to keep in mind that blue carbon will not solve this global problem entirely unless we find ways to stop the release of carbon into the atmosphere. Blue carbon is only an opportunity to mitigate the global climate crisis. And the fate of planet Earth lies in the decisions made by you and me.

IT IS NOT NATURE THAT WANTS HUMANS IN ORDER TO SURVIVE BUT HUMANS WHO DESPERATELY NEED NATURE TO THRIVE!

References

https://climate.nasa.gov/effects/

https://climatekids.nasa.gov/greenhouse-effect/

https://www.thebluecarboninitiative.org/

https://www.whoi.edu/know-your-ocean/ocean-topics/climate-ocean/blue-carbon/

Image courtesy

Featured image

https://images.squarespace-cdn.com/content/v1/5bb9f390da50d330b261fdc8/1626717704901-7BSFO8256SC3ZNS5SSLX/A+Maze+of+Mangroves?format=1000w

Figure 1

https://www.bluecarbonsociety.org/images/home/mangrove.png

Figure 2