Biodiversity: between fragility and sustainability

‘Through its causes and its consequences, the destruction of biodiversity is one of the main drivers in the emergence of zoonoses, diseases of animal origin which are transmissible to humans,’ confirms Benjamin Roche, a biologist from UMI UMMISCO. Certain animal species are in fact a “dead end”; they host the microbes without transmitting the infection to other animals.

‘However, these “cul-de-sac” species are generally among the first to disappear when biodiversity is eroded. This in turn reduces the “dilution” of infectious agents in the environment,’ the biologist explains. Transmission of micro-organisms among wild animals thus becomes more intense. Deforestation and changes in land use also increase contact between this wildlife with a potentially higher rate of infection and humans or domestic animals. This facilitates the direct or indirect transmission of infectious agents to the human population.

Determining the starting point of these zoonoses is key to preventing new pandemics. In the case of COVID-19, SARS-CoV-2 probably originated in bats. ‘Like SARS-CoV-1, which was responsible for the SARSSevere Acute Respiratory Syndrome epidemic in China in 2003, the natural reservoir of this new virus would appear to be an insect-eating bat of the genus Rhinolophus,’ adds virologist Éric Leroy from MIVEGEC UMR. ‘The challenge at present is to identify the chain of events that led to the transmission of animal SARS-CoV-2 to humans. Was it due to direct contact between bats, or their biological fluids, and humans? Or did an intermediary species play a role in the spread of the virus?’  

With an intermediary host, two different strains of coronavirus may have recombined by swapping genetic material. This recombination modifies some characteristics of the virus, such as its transmissibility, and may enable it to ‘jump’ over the barriers between species. The pangolin, a small mammal hunted for its scales and meat, was an initial suspect.

In order to review and coordinate these projects, a multi-institutional consortium has been set up, composed of IRD, the French Agency for Research on AIDS and Viral Hepatitis (ANRS) and INSERM’s REACTing consortium (the merger of the latter two led to the creation of ANRS | Emerging Infectious Diseases in January 2021). ‘In association with researchers from the South, this task force ensures that French actions abroad are in line with the priorities of these countries,’ explains Éric Delaporte, Professor of Infectious Diseases at Montpellier University and Director of the UMI TransVIHMI. He co-chairs the strategic committee of this consortium, alongside Nicolas Meda, Professor of Public Health at Ki-Zerbo Ouagadougou University, Burkina Faso. 

To assess this risk in Africa, the AFRICov project, steered by Philippe Gaubert from EDB UMR and Sery Ernest Gonedelé Bi from the genetics laboratory of Felix Houphouët-Boigny University in Abidjan, is monitoring the genomics of viruses in bush markets throughout Côte d’Ivoire, Cameroon and Benin. Similarly, ZooCov aims to implement a coronavirus monitoring system for the bush meat sector in Cambodia. Led by CIRAD [French Agricultural Research Centre for International Development], this project, which also involves IRD, the Pasteur Institute in Cambodia, Hong Kong University and the NGOs Wildlife Conservation Society and Fauna & Flora International, hopes to contribute to the prevention of future pandemics.

From humans to animals

Anticipating new epidemics is also the aim of the SPILLBACK study, the fruit of collaboration between IRD and the Brazzaville national public health laboratory in the Republic of Congo. ‘With our partners, we have already demonstrated the existence of coronavirus strains in bats in Gabon,’ explains Éric Leroy. ‘We’re now looking to find out whether SARS-CoV-2 can adapt to the wildlife of African tropical forests with a similar climate to that of South-East Asian forests.’ For example, native bat species could become new virus reservoirs and potentially trigger a second pandemic. Farmed animals are also concerned by COVID-19, as shown by the transmission of the disease in mink farms in several fur-producing countries, such as Denmark or the Netherlands. The risk is that ‘the promiscuity of thousands of individuals fosters the emergence of long-term mutations which are transmissible to humans,’ Éric Leroy explains. One such mutation, known as Cluster 5, contaminated several people working in breeding farms.

There is also a threat for companion animals. ‘While few serious forms have been observed to date, cats and dogs of COVID-19 patients present a high risk of contracting the disease,’ comments the virologist, whose team was the first to assess transmission of SARS-CoV-2 from pet owners to their animals in France. Further to this study, the same researchers launched the COVET project, in partnership with the VEBIO veterinary analysis laboratory in Arcueil, the vets from the Paris Vision Institute, and the International Centre for Research in Infectious Diseases (CIRI) in Lyon. ‘The aim is to carry out a serological survey on the infection of several thousand pets, such as dogs, cats and small rodents, across Metropolitan France,’ explains Éric Leroy. Researchers hope to assess the rate of contamination of these animals via their owners, in addition to the variability of infections according to the species. These studies reiterate the relevance of the One Health approach which associates human, animal and environmental health in the fight against zoonoses and their emergence. 

Prevent rather than cure

Let’s be clear, COVID-19 will not be the last pandemic to hit our society. A report by IPBES (see insert), published last year, shows little optimism: future pandemics may be more frequent, spread more rapidly, and have bigger impacts on the world economy. Above all, they will claim more victims than COVID-19! In addition, mammals and birds carry hundreds of thousands of viruses which have yet to be discovered and are potentially transmissible to humans. Benjamin Roche, who contributed to drafting this report, notes that ‘solutions do exist, such as the creation of an international institution to fight against pandemics, the institutionalisation of the One Health approach, and the reduction of contact between humans, wildlife and domestic animals.’ In practical terms, this may mean managing the wildlife trade, creating protected areas, particularly in regions with the highest levels of biodiversity, or taxing pro-pandemic activities such as deforestation or intensive farming.

Pathogenic episodes have devastated agricultural crops in the past. Such is the case of blight, which appeared in Ireland in 1845. This disease is caused by a parasite, Phytophthora infestans, and attacks potato plants in particular. ‘Monoculture of this tuber allowed the pathogen to spread rapidly throughout the country,’ explains Jean-Louis Pham, a plant geneticist at DIADE UMR. ‘The demographic and cultural consequences were dramatic.’ The fall in crop yield due to blight played a major role in triggering a famine which lasted for several years. Current studies estimate that it caused at least a million deaths and the mass migration of two million Irish people.  

However, the IPPC does not avail of a truly operational international network to monitor plant disease similar to that set up by the World Health Organisation to raise the alert in the event of human epidemics. In addition to heightened vigilance, the choice of local intra-varietal lineages, instead of pure lineages, limits the emergence of epidemics. ‘Domesticated species generally present little genetic diversity and are therefore more vulnerable to diseases,’ Jean-Louis Pham explains. As a recent study on sweet potato has confirmed, genetic diversity is the foundation stone which enables a species to adapt to disease and changes, in climate for example. Several initiatives have been launched to preserve this diversity. One such is ARCAD, the resource centre for the conservation and study of diversity in tropical and Mediterranean crops. Based in Montpellier on the Agropolis campus, ARCAD rallies the support of IRD, CIRAD, INRAE and Montpellier SupAgro around a common project focused on transdisciplinary agro-biodiversity. ‘Scientists from all backgrounds, geneticists, bioinformaticians, agronomists, botanists, anthropologists and political science researchers, work together to bring new momentum to research in agro-biodiversity,’ says Jean-Louis Pham, a co-founder of the project. ‘One of the aims is to innovate in the use of plant biodiversity, in particular by promoting the wealth of Southern seed production.’ A building has been created for this purpose, and will eventually conserve up to 40,000 seeds. ARCAD also acts as an exchange platform between the academic world and civil society, both nationally and internationally. ‘It’s vital to re-establish the flow between seed collections and farmers’ fields.’  

The move towards agro-ecological transition

In fact, it is in a certain number of these fields that part of biodiversity is being undermined. The industrialisation of agriculture, characterised among other factors by growing use of petrochemical-based inputsAll plant treatment and fertiliser products added to soil and crops which do not come from farming operations and the creation of vast plots through land consolidation, result in standardisation of rural landscapes and the species that are cultivated. 

Among these organisms, there is one emblematic species for soil health: the earthworm. The earthworm plays several key roles. ‘Earthworms contribute to soil structure and recycling organic matter, as well as providing plants with the minerals they need to grow, such as nitrogen and phosphorus,’ the ecologist explains. This underground world works in harmony to change the dynamics and composition of soils, making them more fertile, minimising erosion and facilitating rainwater drainage. How can we protect the soil and the services it provides to agriculture? First, ‘sowing cover plants after the harvest avoids exposing bare ground for a large part of the year,’ says Sébastien Barot. One plant family, the fabacae, known more familiarly as legumes, is particularly well-suited to this task. This large plant family, which also includes clover, alfalfa, soya, peanut and numerous other pulses, enriches the soil naturally by fixing nitrogen from the air, thanks to a symbiotic relation with the soil bacteria Bradyrhizobiums. In addition to producing plant-based protein which feeds livestock, poultry and humans, these plants also reduce the need for fertilisers. 

‘Agro-forestry systems act in complement and symbiosis to produce differently and better. Sustainable livestock rearing in farmland woods, for example, has less impact on climate and produces meat with a higher nutritional quality,’ the ethno-botanist adds. In temperate regions, these agro-forestry production methods were largely abandoned following the industrialisation of agriculture. In France, for instance, 70% of hedgerows have disappeared from bocages since the 1950s. Geneviève Michon deplores the fact that ‘trees are still being cut down and hedgerows uprooted.’ Nevertheless, the situation is changing and methods inspired by long-abandoned know-how have been revived in certain areas, with bocages, orchard meadows or pairings between trees, vine or hops. 

However, certain forms of orally-transmitted knowledge, such as traditional pharmacopoeia, are in danger. IRD is committed to perpetuating some of this expertise, specifically in Guiana or with the Yanesha of Peru. ‘In this Amerindian community, the transmission of knowledge comes up, among other factors, against a certain degree of disinterest on the part of young generations,’ explains Mohamed Haddad, a chemist specialised in the study of natural substances at PHARMA-DEV UMR, who has lived with the Yanesha on several occasions. ‘With a view to conserving their heritage, these Amerindians have accepted, in partnership with the scientific community, to catalogue a part of the plants they use for medicinal, cosmetic or ritual purposes.’ Initiated in 2005 by ethno-pharmacologists Geneviève Bourdy and Céline Valadeau, this collaboration culminated in the publication of a freely accessible book, ‘Yato' ramuesh’. Financed by public funding with the consent of the Peruvian authorities, ‘this work, which was widely-acclaimed by the community, has allowed us to record a part of their knowledge.’ This is a perfect example of mutual trust between researchers and a local community. However, the potential value of some biological resources and associated local knowledge can be subjected to abuse and unilateral exploitation. The principle of ‘access to genetic resources and associated traditional knowledge and the fair and equitable sharing of the benefits arising out of their use,’ or ABS, was established to avoid this form of illegitimate monopolization

In the 1990s, the US government thus cancelled part of Jamaica’s debt in exchange for the creation and funding of a foundation for the environment. ‘There is a renewed interest in this tool due to growing debt linked to the pandemic, and it is also a benchmark device in the fight against climate change,’ says SENS UMR economist Philippe Méral. On a local level, there is a whole array of public policies to promote the preservation of nature, such as Payments for Environmental Services (PES). ‘The idea is to remunerate people, either individually or collectively, who can maintain ecosystems in a healthy state for those who benefit from their ecosystem services,’ Philippe Méral explains. ‘These payments help to prioritise conservation over over-exploitation, which, while offering short-term economic benefits, causes harmful ecological and social consequences in the long term.’ In practical terms, PES can take on various forms, but they often imply the prevention of deforestation in order to protect bio-diversity, capture carbon or maintain the water quality and drainage in the downstream parts of river basins. Although highly popular among NGOs and donors around a decade ago, this tool has since lost its appeal. ‘Payments can alter the intrinsic motivations of individuals to preserve their environment and can aggravate issues of equity between generations,’ observes the expert in environmental policies, ‘but above all, it is not a lever for development, contrary to other income-generating activities such as craftwork, medicinal and herbal plant harvesting, or eco-tourism.’ Depending on the context, this type of economic incentive for biodiversity may be more suited to reconciling environmental conservation and socio-economic growth. This is also the case for community management, which is based on a sustainable use of resources thanks to agreements between users. In addition to moderate economic growth, another limiting aspect of PES is their funding. To ensure long-term funding, the trust fund is a useful lever. ‘In this case, a significant sum of money from an NGO or donor is placed in a foundation and only the interest earned is used for environmental protection,’ the economist explains. ‘This system secures the investment, but is a relatively complicated mechanism which raises ethical issues.’ As the funds are floated on the stock market, interest depends on the volatility of rates and the capital invested may be lost in the event of a market crash. However, trust funds have gained in popularity in recent years, not only to ensure the funding of PES, but also that of protected areas and other economic tools for the conservation of biodiversity.

In this region, a 53-year-old Ecuadorian, Anelio Loor, owns a small plot of a few hectares, which he is safe-guarding from intensive farming. Located in the Manabí province, almost 200km west of Quito, ‘La Esperanza’ or the ‘Reserve of Hope’, as Anelio Loor calls it, lies on a small hill crossed by a river. ‘It feels like a rainforest in the heart of this reserve,’ says Thomas Couvreur, a botanist at DIADE UMR, who met the farmer during a mission to collect palm tree samples. ‘Hundreds of animal and plant species, including endangered species, have been observed there. It’s hard to believe it’s just 500 metres from a tarmac roadway.’ For 23 years, with neither funding nor aid from an NGO, Anelio Loor has put his heart and soul into protecting this small haven of nature that he bought with his own savings. He would like to go further, however, and turn his reserve into a tool for science. ‘Anelio has built a research station to work with botanists and zoologists, and has installed facilities to welcome students.’ Projects are already under way, in close collaboration notably with the Pontificia Universidad Católica del Ecuador in Quito, for whom he has already worked as a para-taxonomist (a local expert in the collection and inventory of biodiversity, without official scientific or academic training) in the Yasuni National Park. ‘Anelio is a very humble person, but is driven by fascination and love for biodiversity,’ Thomas Couvreur adds. This nature lover is also actively looking for funds to save a plot of forest next to his reserve from deforestation, and thus perpetuate ‘La Esperanza’.

At present, this activity is threatened by over-exploitation of stocks and the degradation of mangroves. To protect it, new regulations have been implemented in recent years, including a total ban on the use of mangrove wood, an annual fishing closure and an increase in the minimum size of crabs authorised for sale. ‘Are these measures effective, sufficient and legitimate? They raise questions, particularly among poor populations for whom crab fishing is a matter of survival,’ Marc Léopold emphasises. 

The current market has shifted towards high-added-value exports of live crabs, primarily for the Chinese market. However, fishermen and small-scale operators believe that the local economic benefits are insufficient. ‘A collective survey of the sector’s organisation, regulations and local management methods, in addition to the socio-economic impact on households is under way,’ says the researcher. With regard to the environmental aspect, awareness will be raised among fishermen and operators on the limits of biological regeneration of the crab population and on the links between fishing practices and the mangrove. The ultimate aim is that improved management all along the chain will enable vulnerable communities to gain from this resource without degrading its natural environment.

However, fishery products represent a key source of nutrition to feed a growing world population. Fish farming has been widely developed in response to this need. At present, aquaculture production is on a par with fishing. However, like over-fishing, the intensive development of fish farming has also impacted marine environments. Fish excrement and uneaten feed contribute to eutrophication of water, for example; algae flourish and the amount of oxygen in the water decreases. Farmed species can also escape into the natural environment and become invasive. Furthermore, the high density of specimens in farming ponds facilitates the spread of pathogens. One solution is to administer antibiotics, but their residues cause hormonal disorders in aquatic species and contribute to the phenomenon of antibiotic resistance. Lastly, some farmed fish are fed on industrial fish catches. A case of the fish biting its own tail!

AfriMAQUA aims to tackle all these challenges facing marine aquaculture in Africa, a continent where such activity is still very limited. ‘This research consortium is hoping to develop sustainable aquaculture by exchanging knowledge, building partners’ capacities and pooling research efforts,’ Maria Darias, the scientific coordinator of the network, explains. AfriMAQUA has already brought together teams from Senegal, Côte d’Ivoire, Namibia, South Africa, Tanzania, Kenya and Mauritius. 

The 5th edition of the Global Biodiversity Outlook published in 2020 by the CBD draws a bleak conclusion on the United Nations Decade on Biodiversity. Not one of the twenty Aichi Goals set in 2010 in Nagoya to protect nature has been fully reached and the erosion of biodiversity continues. Yet the importance of biodiversity in ensuring the long-term food security of the world and limiting the emergence of future pandemics is an irrefutable fact. Time is running out, however. ‘If ambitious action is not taken by 2030, either the damage inflicted on biodiversity will be irreversible, or the cost of restoring ecosystems will be too high for society,’ Yunne Shin warns. With a group of experts commissioned by Future Earth, a worldwide network of scientists devoted to sustainable development, the biologist participated in drafting an opinion piece for the journal ‘Science’ which puts forward more effective solutions than those of Aichi to ensure global protection of biodiversity and ecosystems. This is the real issue for COP15, scheduled from 11 to 24 October in Kunming, China: to define a bold strategy for the preservation of biodiversity in the coming decade. 

Other sensitive issues are to be raised during COP15, including the protection of 30% of natural areas by 2030, brought to the table by NGOs and the High Ambition Coalition for Nature and People, coordinated by France and Costa Rica. Yet serious doubts remain as to the relevance of this initiative, in particular with regard to its cost, proven benefits and practical implementation. ‘The creation of protected areas does not solve the issues of climate change or pollution,’ geographer Estienne Rodary comments. He believes this conservation model may be obsolete. ‘Does protecting a part of the planet mean we can damage the rest?’ Developing countries are nonetheless willing to accept the principle of 30% protected areas if compensation is granted to them on a sovereign level. In particular, they request that DSI or Digital Sequence InformationDelocalised genetic sequences that can be used in the same way as genetic resources extracted directly from biodiversity be taken into account in the Nagoya Protocol on the same level as genetic resources. The matter of protecting marine biodiversity outside exclusive economic zones (EEZ) will also be raised. However, it is the ‘mainstreaming’ of biodiversity that will remain the key issue. ‘Like climate, biodiversity must be integrated into all areas of public policy,’ Estienne Rodary argues. Although the solutions may be local and depend on local conditions and needs, action on a global scale is essential to halt the decline in biodiversity and foster the hope that humans may live in harmony with nature by 2050.

"Biodiversity in the global south - Research for a sustainable world", is a richly illustrated publication by IRD, geared towards a wide audience and coordinated by a scientific committee of more than 40 researchers.

In a modern world faced with climate change and pandemics such as COVID-19 linked to the decline of natural environments, how does research contribute to preserving nature?

Discover the key challenges in preserving biodiversity through 25 examples of multi-disciplinary studies, led by IRD researchers and their partners.