Integrated omics for increasing plant production and health‐related nutrition under extreme conditions: The Indonesia perspective

Climate-smart agriculture and forestry: maintaining plant productivity in a changing world while minimizing production system effects on climate.

Biodiversity is endangered in many regions of the world, with loss of native plant species a growing concern requiring a major focus on conservation measures. However, the threat posed by introduced viral pathogens to native plant biodiversity has been ignored almost completely. What occurs when weed seeds and vegetative propagules or seeds of cultivated plants unknowingly infected with viruses are introduced to other regions of the world and the viruses introduced with them then invade indigenous plants for the first time? To what extent are introduced viruses capable of causing damaging diseases which then threaten native plant communities and their species biodiversity, and in what ways can they do this? What can be done about it? In this Opinion piece, our intent is to answer these questions by awakening worldwide interest to undertake research activities that provide a comprehensive understanding of the threat posed by introduced viruses to natural plant ecosystems and biodiversity. Development of such an understanding requires research activities capable of providing in-depth information at both biological and molecular levels. Without such knowledge, effective solutions are unlikely to emerge. New encounters involving viruses and plant species are becoming increasingly common at the agro-ecological interface between managed and natural vegetation. This is because of rapidly increasing human activity, such as agricultural extensification, diversification and intensification practices to increase food production and to address food insecurity, encroaching urbanization and ever increasing international trade in plants and plant products (e.g. Alexander et al., 2014; Jones, 2009, 2014; Roossinck and Garcia-Arenal, 2015). Moreover, inadvertent introduction of new, more efficient virus vectors often exacerbates spread of viruses to previously uninvaded plant species at vegetation interfaces. In the future, the frequency of new encounters between viruses and plant species is likely to increase even more rapidly because of the major alterations in cultivated plant distributions anticipated from climate change (Jones and Barbetti, 2012). Genomic divergence is roughly proportional to the evolutionary distance from a common ancestor, and a high degree of nucleotide sequence diversity over a small geographical range is typical of viruses that have co-evolved locally with native plants (e.g. Coutts et al., 2011; Webster et al., 2007). These viruses are referred to as ‘indigenous’ to distinguish them from others that have arrived from elsewhere and therefore show much less sequence diversity, for which the term ‘introduced’ is used (e.g. Coutts et al., 2011; Jones, 2009; Webster et al., 2007). The threat posed by introduced fungal pathogens to native plant communities and their biodiversity has received considerable attention (e.g. Burdon et al., 2006), and the consequences of virus infection seem likely to resemble those of fungi, including a reduced ability of infected plants to compete with other plants and produce sufficient seed for the next generation (e.g. Cooper and Jones, 2006). However, the threat posed by introduced viral pathogens has received much less attention (Vincent et al., 2014). This is so despite the considerable research activity aimed at understanding how emerging viruses spread in the opposite direction, i.e. from native plants to damage introduced cultivated plant species, especially in the tropics. Such studies normally involve investigation of new encounter scenarios at the agro-ecological interface (e.g. Alexander et al., 2014; Jones, 2009; Roossinck and Garcia-Arenal, 2015). Native plants do not grow as stands of genetically identical plants of the same species exhibiting uniform virus susceptibilities, but as mixed species communities exhibiting both withinand between-species diversity. Natural control measures which serve to decrease virus spread in undisturbed native plant communities, such as mixture with non-hosts, isolation, host resistance/tolerance and the presence of predators and parasites of their vectors, tend to be disrupted when such communities are disturbed,as occurs at the agro-ecological interface and in otherwise disturbed natural vegetation (e.g. Cooper and Jones, 2006; Jones 2009). Co-evolution of viruses with their plant hosts and vectors is thought to have been underway since plants first appeared (Fraile and Garcia-Arenal, 2010; Lovisolo et al., 2003). Thus, long before plants were first domesticated by former hunter gatherers when agriculture began 10 000–15 000 years ago, plants were co-evolving with native plants growing in different world regions. This co-evolutionary process moulded both viruses and native plants (e.g. Vincent et al., 2014). In undisturbed native plant *Correspondence: Email: roger.jones@uwa.edu.au bs_bs_banner

Productivity, water use and climate resilience of alternative cocoa cultivation systems

Does a Warmer World Mean a Greener World? Not Likely!

In Indonesia, the monitoring of Greenhouse Gases (GHGs) is a vital part of the nation's planning strategy, primarily spearheaded by the Meteorological, Climatological, and Geophysical Agency (BMKG) in response to the World Meteorological Organization's (WMO) mandate through the Global Atmosphere Watch (GAW) program. This initiative is of paramount importance as it aims to provide comprehensive and robust GHG monitoring to support global and national efforts in understanding and combating climate change. Despite existing efforts, there remains a pressing need to expand these services to ensure more accurate and extensive data collection, which is crucial for informing government policies and international climate negotiations. Indonesia's approach to GHG monitoring is multifaceted, encompassing global, national, and sub-national strategies to provide a comprehensive understanding of GHG dynamics and contribute effectively to global efforts. At a global and regional level, Indonesia boasts the longest GHG dataset in Southeast Asia, as well as in the equatorial region, from Bukit Kototabang. This data is invaluable, feeding into the WMO GAW international network and providing insights that aid in refining GHG inventories worldwide. It represents a significant contribution to the global understanding of GHG trends and helps position Indonesia as a critical player in international climate dialogues, especially concerning carbon budgeting and emission reduction strategies. Additionally, the implementation plan for the Global Greenhouse Gas Watch (G3W) program, a WMO initiative for a GHG monitoring effort worldwide,  is incorporated in the nation’s GHG monitoring plan, aiming for a more inclusive and extensive GHG monitoring network. Nationally, Indonesia's strategy leverages the potential of satellite-driven information.  This approach can be considered as complementary as it offers an advantage in providing better spatial resolution, and fully representing the differences in land-cover types. At a sub-national level, the focus is on atmospheric-based monitoring to provide localized GHG estimates through a roadmap for the adoption of the Integrated Global Greenhouse Gas Information System (IG3IS). This ambitious program aims to monitor atmospheric GHGs in an integrated manner, combining this with atmospheric modeling to yield a range of benefits. It enables the estimation of carbon emissions across various sectors and complement in calculating carbon sequestration, particularly in forestry initiatives. Together, these strategies illustrate Indonesia's nuanced and robust approach to GHG monitoring. By continuously enhancing its GHG monitoring plans, adopting advanced satellite technology, and focusing on localized atmospheric monitoring, Indonesia not only contributes valuable data to the global scientific community but also strengthens its own capacity to address climate change. This integrated approach is crucial for developing a comprehensive understanding of GHG dynamics, informing policy and international negotiations, and ultimately guiding the nation towards a sustainable and resilient future in the face of global environmental challenges. 

Enhancing sustainability of grassland ecosystems through ecological restoration and grazing management in an era of climate change on Qinghai-Tibetan Plateau

Brazil is a megadiverse country with continental dimensions. It is long acknowledged as the richest country in plant diversity, encompassing approximately 20% of the world’s flora, with more than 50,000 species of plants, algae and fungi distributed in six major biomes, including two biodiversity hotspots. However, significant environmental challenges, primarily driven by climate changes and intensive, non-sustainable land use practices, have led to widespread deforestation, habitat reduction and, consequently, shifts in species distribution, genetic erosion and increased vulnerability. Considering the high rates of endemism and the global economic value of numerous Brazilian native species as crops and wild relatives, ornamentals and medicinal plants, cryopreservation emerges as a fundamental ex situ complementary strategy to safeguard its plant genetic resources. This article aims to provide a comprehensive overview of cryopreservation of native plants in Brazil during the past decade, which shows that more than 85 species from 23 families have been cryopreserved. Methods for assessing cryoinjury at the morphophysiological, biochemical, molecular and metabolic levels are reviewed. The main challenges, as well as future perspectives for the cryopreservation of Brazilian floristic diversity, are also discussed.

Climate Change, Connectivity, and Conservation Success

The paper discusses plant conservation strategies for protecting endangered species. It highlights the importance of plant biodiversity, its significance, and the consequences of its loss. The abstract also outlines various conservation techniques, including in-situ and ex-situ protection, specific management systems, and biotechnological methods. Additionally, it touches on the causes of extinction risk to plant biodiversity, such as habitat destruction, climate change, overexploitation, invasive species, and pollution. The abstract emphasizes the need for conservation efforts to protect endangered plant species and preserve biodiversity. The following items were explained: 1. Plant biodiversity is essential for ecosystem functioning and human well-being, 2. Human activities, such as habitat destruction, climate change, and overexploitation, threaten plant biodiversity, 3. Conservation techniques, including in-situ and ex-situ protection, specific management systems, and biotechnological methods, can help protect endangered plant species, 4. Community awareness and participation, research, and monitoring are crucial for effective conservation, 5. The loss of plant biodiversity can have severe consequences, including reduced food security, decreased ecosystem resilience, and negative impacts on human health.

Species are disappearing at a rate comparable with previous mass extinctions. Freshwater environments are being particularly affected, with biodiversity losses occurring much faster in freshwater than in terrestrial or marine ecosystems. This study assessed the research on drivers of biodiversity loss in freshwater environments as described in nearly 37,000 articles published in the last decade. Articles on biodiversity published between 2010 and 2019 were retrieved from the Web of Science to determine the number of articles that addressed a particular driver of biodiversity loss, by analysing the titles, abstracts, and keywords. The biodiversity and development status of a country was also investigated to see how it affects its scientific output (i.e. number of published articles). Twenty per cent of the articles on biodiversity addressed freshwater biodiversity. Researchers devoted considerable effort to six drivers – climate change, water pollution, flow modification, expanding hydropower, species invasions, and habitat degradation – but practically ignored other threats, such as plastic and light pollution. It was also found that megadiverse countries, which for the most part were also developing countries, published substantially fewer articles than developed but less biodiverse countries. We recommend a series of actions that could contribute to mitigate the biases found in this study.

Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.

Forest management can mitigate negative impacts of climate and land-use change on plant biodiversity: Insights from the Republic of Korea

The root–microbe–soil interface: new tools for sustainable plant production

Conventional methods for probing molecular changes in condensed matter systems, such as electronic and vibrational spectroscopy, are difficult to implement at the extreme conditions associated with dynamic compression experiments. This is particularly true for experiments in the multimegabar regime; to achieve the requisite energy density to produce such pressures, sample sizes are necessarily quite small and experimental timescales are, therefore, extremely short. Furthermore, these extreme pressure conditions also result in high temperatures and, therefore, significant thermal emission even in the visible to infrared regime and in some cases render the sample opaque or reflective, thereby precluding bulk spectroscopy techniques, such as Raman scattering. These experimental challenges require a different approach to evaluating shock-induced changes at the molecular or atomic level in the multimegabar or the so-called warm dense matter regime. The past few decades have seen significant advances in the use of first-principles methods to investigate materials under extreme conditions, enabling these methods to become a powerful tool for exploring molecular systems at extreme conditions. Here, we discuss the construct of combining high-precision shock wave experiments with first-principles theory to explore molecular systems at extreme conditions. The results from high-fidelity dynamic compression experiments are used to evaluate first-principles theoretical frameworks and identify the framework that best reproduces experimental results in the regime of interest. That validated framework is then used to perform detailed simulations of the system of interest, providing unique insight into the response of the system at the molecular level.

Four Commentaries on the Pope’s Message on Climate Change and Income Inequality. IV. Pope Francis’ Encyclical Letter Laudato Si’, Global Environmental Risks, and the Future of Humanity.