Introducing the Rewilding and Restoration Collection

As we approach the beginning of the UN Decade on Ecosystem RestorationPLOS ONE and a team of dedicated Guest Editors have brought together a Collection of research showcasing current practical and theoretical approaches to rewilding and ecological restoration around the world. The Collection features a wealth of interdisciplinary research covering systems from forests to wetlands, and addressing issues from species reintroductions to public perceptions. Fourteen research articles are included in the Collection at launch, but more will be added in the coming months, so keep checking back for updates!

PLOS ONE is hugely grateful to all who have participated in this Collection, especially our fantastic Guest Editors.

Featured image: Austin D on Unsplash

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Amphibians and reptiles on the edge: An interview with intrepid PLOS ONE authors

Amphibians and reptiles are among the world’s most extraordinary and most threatened animals. In this post, we highlight work recently published in PLOS ONE by Rivas and colleagues, which probes the diversity of species in an understudied region at the northernmost extremity of South America. We spoke with the authors about their research and its broader context.

What was the motivation for your study? 

Initially, the study aimed to understand the composition of the reptiles and amphibians of a region in northeastern Venezuela, namely the Paria Peninsula and surrounding mountains. However, along the way, many other questions stared emerging concerning the composition and faunal relationships of the whole region, so we aimed to compare the herpetological composition of all the northernmost coastal mountains of South America, ranging from northeastern Colombia through Venezuela to the Caribbean islands of Trinidad and Tobago, totaling about 1000 km east to west.

 Map of northern South America showing locations of the sampling sites. pone.0246829

How did you get to the sampling locations? Were there any challenges with the fieldwork? 

We sampled in eastern Venezuela (Paria Peninsula), which had already been visited by some of us for about 20 years. We visited some locations in central and western Venezuela, and we had exhaustive literature records and museum revisions at our hands. Similarly, records from Trinidad and Tobago were available from three decades of field trips carried out by some of us as well as through the University of the West Indies and Glasgow University students and staff members. This study was only possible though decades of expeditions and fieldwork in the region by several of the authors of this paper. There were many challenges, especially in Venezuela, such as those related to transport, lack of fuel, increased travel costs, insecurity and remoteness of some of the sampling sites. Fortunately, safety was always supported by local agencies and communities in eastern Venezuela. In addition, funding was at the time lacking or limited for fieldwork in Venezuela and Trinidad, and travel expenses at times were privately funded by ourselves.

Could you briefly describe the key findings of your study and their importance? Were there any surprises? 

This is the first study to address the biogeographic patterns of any vertebrates in the region at this scale. We ultimately recorded a total of 294 native species distributed above 200 m in elevation along all the mountain systems. The biogeographic composition supports close species associations for both reptiles and amphibians within regions, such as western areas (northeastern Colombia and western Venezuela) versus eastern localities (eastern Venezuela and Trinidad and Tobago). Our biogeographical findings support the geological history, with the whole region once being a mountain chain that connected all the way up to Tobago, and biogeographical patterns following a natural topographic disposition. However, when we compared species at high elevations, the arrangements were more unstable, with lower numbers of species shared between areas and a minimal association between areas. This suggests that faunal patterns at higher elevations represent more exclusive species which are less useful to assess biogeographic relationships in the region. Overall, the high diversity of reptile species found throughout the study area reflects their dispersal capability and the presence of habitat generalists when compared to the more restricted and ecologically constrained amphibians.

Vegetation in Venezuela’s northernmost montane coastal systems. pone.0246829

What are the main threats to species and ecosystems in the region? 

In northern Venezuela the habitat loss is mostly due to logging, illegal crops, and livestock, and to a lesser degree mining, particularly in lower and medium elevations in some mountains. In eastern Venezuela, the most threatened environments are the cloud forest, and it’s increasingly common to find local crops, even within protected areas, putting pressure on the very much depleted hydric resources of some areas. We have encountered small-scale crops at elevations of up to 1500 m. More worrisome is the fact that several illegal crops do not even belong to local villagers but to farmers from the lowland towns, which are increasingly looking for higher and fresher locations for their crops. Low altitude tropical cloud forests such as those found in the Paria Peninsula and in Trinidad are among the most vulnerable terrestrial ecosystems to climate change. Some cloud forests have exceptional low altitudinal ranges and require detailed species inventories, population assessments, and the establishment of new, well-run national parks to protect biodiversity. In addition the lack of scientific funding in the region is limiting the understanding of this biodiversity hotspot.

How can scientific research help us better understand and protect biodiversity in this region? 

This and previous studies undertaken by some co-authors are increasingly important to understand the importance of these ecosystems on a wider scale. These mountains can be viewed as the northeastern natural extension of the Andes chain, but due to their relatively low altitude, they have been undervalued in terms of their biodiversity and biogeographical relevance. In addition, surveys help establish species checklists and report on endemism in the region. Taxonomic studies based partly on phylogenetic analyses are key to assess the high rate of cryptic species in the region. Through species descriptions, understanding of population ranges and biogeographic barriers can help establish new areas that need protection. Furthermore, there seems to be little research on ecological studies at a broader scale in the region. In addition, little is known in this region compared to that of The Guianas or Brazil.

Future research should have an important conservation component, as well as the involvement of citizen research. Environmental education with a strong conservation focus must be a priority and be consistently delivered to local communities, which also applies to most Venezuelan national parks. Finally, ecotourism could help establish new sources of income in the region, although the political, economic and safety situation in Venezuela, and to a lesser degree in Trinidad, are obstacles to its development. An important contribution to the preservation of the national parks would be to finish the zoning rules and increase the expansion of some parks. New surveys and effective and consistent monitoring of the parks and other areas are urgently needed in Venezuela.

Some Trinidad amphibians and reptiles. pone.0246829

What is the importance of Open Access for your field of research and the regions where you work? 

Without Open Access this research would be visible to a limited audience, mostly within academic institutions in the developed world, and not to local policymakers and scientists.

 What should be the priorities for future research in this area? 

As mentioned earlier the understanding of species distributions and identification is key to understand if the national parks’ delimitations are correct and if new areas should be protected. Application of molecular techniques will be a priority as much local research is based on the more traditional sciences, and there seems to be a lack of capacity in molecular techniques in Trinidad and Tobago and Venezuela. Universities should benefit from a new generation of researchers that are specialized in contemporary ecological, conservation and molecular techniques. Throughout the elaboration of this study, we had to compile a great amount of available literature on the region and it soon became apparent that most works from Venezuela were on average several decades old and some pioneering works in the region had no follow-ups since their publication. This is a reminder of the poor understanding of biodiversity in the region, in part due to the challenging socioeconomic circumstances.  


Rivas GA, Lasso-Alcalá OM, Rodríguez-Olarte D, De Freitas M, Murphy JC, Pizzigalli C, et al. (2021) Biogeographical patterns of amphibians and reptiles in the northernmost coastal montane complex of South America. PLoS ONE 16(3): e0246829.

Featured image:
El Tucuche, Trinidad- Jamie Males.

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Introducing the Plant Phenomics & Precision Agriculture Collection

We are very excited to launch our new Collection on Plant Phenomics and Precision Agriculture. Our Guest Editors- Malia Gehan, Guillaume Lobet and Sierra Young- have curated a diverse group of research articles selected from the pool of submissions we received in response to our call for papers. Here we highlight some of the articles included in the Collection at launch- but more will be added in time, so do keep checking back!

We start our tour underground. Measurement of belowground plant traits requires specialised technological solutions to overcome the challenges posed by the physical properties and variability of substrates. Adu and colleagues measured root architecture traits of young pot-grown cassava plants, with the aim of identifying appropriate yield predictors for mature field-grown plants [1]. They found strong evidence for the feasibility of their phenomic approach as a means for exploring yield components.

Other belowground structures were studied by Kudenov and colleagues [2]. They demonstrated the potential of interactance spectroscopy for probing the internal tissues of sweet potatoes in order to identify defects that affect culinary value and storage quality. The technique was effective to depths of approximately 5 mm, and could represent a significant improvement over current destructive methods for defect monitoring.

Necrotic tissue RGB cross-sectional images from

Machine learning has found a wide range of applications in plant phenomics and precision agriculture, including image-based plant classification. However, all such applications require appropriate training data for the particular crop and task involved. To address this bottleneck, Beck and colleagues developed an embedded robotic system that can automatically generate and label plant images for machine learning applications [3]. The system presented in their Collection article could dramatically increase the efficiency of machine learning-based phenomics.

Full view of the EAGL-I system from

Image segmentation is another key area of research in plant phenomics, underpinning many approaches to analysis of crop growth and development. Li and colleagues described a new end-to-end segmentation system based on convolutional neural networks to support high-throughput phenotyping of maize plants [4]. This system allows for identification of individual plant shoots within a field and extraction of their phenotypes, which could help facilitate progress in varietal selection.

Overview of the image acquisition system from

Another segmentation approach based on near-infrared spectroscopy is presented by Colorado and colleagues in their Collection article [5]. They demonstrate its application for the measurement of aboveground biomass in rice crops. When compared with an existing k-means-based method, the new technique showed a 13% improvement in the strength of the correlation between image-derived and actual biomass.

The UAV system from

Crop mixtures, an important component of many agroecological land-use practices, represent a challenge for image analysis. Focussing on a model grass-legume mixed pasture system, Ball and colleagues used RGB imaging to predict growth and the level of interspecies facilitation [6]. They found that high-throughput phenotyping provides a valuable tool for exploring interactions between species in such complex agricultural environments.

Pot-level separation of plant biomass from

Herbivory is a major challenge to crop growth, and methods for measuring herbivores’ effects on plant health status are therefore vital for screening for resilient crop varieties. The results of a study by Horgan and colleagues suggest that changes in plant reflectance properties caused by planthopper feeding could provide the basis for high-throughput approaches to screening for resistance to sap-sucking insects in cereals [7]. They discuss how such measurements could be integrated in bulk phenotyping tests.

The nutrients available to a crop are another key determinant of performance. Understanding the nutritional composition of any organic soil amendments (e.g. manure, compost) is therefore of critical importance. In their Collection article, Towett and colleagues present a machine learning-based method for quantifying nutrients in organic soil amendments using X-ray fluorescence and mid-infrared spectroscopy [8]. They suggest that portable spectrometers coupled with machine learning algorithms could even be developed as a low-cost tool for use by smallholder farmers.

Several papers in the Collection focus on the potential of unmanned aerial vehicles (UAVs) for phenotyping and surveillance of crop status. In their study, Grüner and colleagues tested whether UAV-based multispectral and textural monitoring could predict aboveground biomass and nitrogen fixation in grass-legume mixtures [9]. Their results showed great promise for this approach, with strong evidence for the importance of including textural information in prediction models.

Orthomosaic of the experimental field from

Meanwhile, Cao and colleagues used UAV hyperspectral remote sensing to model the chlorophyll content of rice canopies [10]. Chlorophyll content is an important indicator of growth status and photosynthetic capacity, particularly under different environmental conditions. The authors used an inversion model based on machine learning, which produced encouraging results supporting the use of such technologies for chlorophyll monitoring.

The UAV hyperspectral imaging system from

Automated monitoring of plant growth in space and time poses many technical difficulties. In recent years, three-dimensional point clouds derived from laser scanners and depth cameras have been used for measuring plant structure, but tracking points over time during plant growth is challenging. In their paper, Chebrolu and colleagues explore the feasibility of a non-rigid registration approach, finding that it could successfully model plant growth in four dimensions and prove useful in automated trait analysis [11].

4D registration of a point cloud pair for maize and tomato from

Last but not least in the first batch of papers included in the Collection, Jacques and colleagues highlight the issue of variability in the properties of materials commonly used in phenomic applications [12]. They show that the production location of a gelling agent used in Arabidopsis seedling phenotyping has a significant effect on the results obtained, affecting the comparability of studies performed using product from different sources.

More articles will be added to the Collection over the coming months, so please do check back for updates!


  1. Adu MO, Asare PA, Yawson DO, Nyarko MA, Abdul Razak A, Kusi AK, et al. (2020) The search for yield predictors for mature field-grown plants from juvenile pot-grown cassava (Manihot esculenta Crantz). PLoS ONE 15(5): e0232595.
  2. Kudenov MW, Scarboro CG, Altaqui A, Boyette M, Yencho GC, Williams CM (2021) Internal defect scanning of sweetpotatoes using interactance spectroscopy. PLoS ONE 16(2): e0246872.
  3. Beck MA, Liu C-Y, Bidinosti CP, Henry CJ, Godee CM, Ajmani M (2020) An embedded system for the automated generation of labeled plant images to enable machine learning applications in agriculture. PLoS ONE 15(12): e0243923.
  4. Li Y, Wen W, Guo X, Yu Z, Gu S, Yan H, et al. (2021) High-throughput phenotyping analysis of maize at the seedling stage using end-to-end segmentation network. PLoS ONE 16(1): e0241528.
  5. Ball KR, Power SA, Brien C, Woodin S, Jewell N, Berger B, et al. (2020) High-throughput, image-based phenotyping reveals nutrient-dependent growth facilitation in a grass-legume mixture. PLoS ONE 15(10): e0239673.
  6. Colorado JD, Calderon F, Mendez D, Petro E, Rojas JP, Correa ES, et al. (2020) A novel NIR-image segmentation method for the precise estimation of above-ground biomass in rice crops. PLoS ONE 15(10): e0239591.
  7. Horgan FG, Jauregui A, Peñalver Cruz A, Crisol Martínez E, Bernal CC (2020) Changes in reflectance of rice seedlings during planthopper feeding as detected by digital camera: Potential applications for high-throughput phenotyping. PLoS ONE 15(8): e0238173.
  8. Towett EK, Drake LB, Acquah GE, Haefele SM, McGrath SP, Shepherd KD (2020) Comprehensive nutrient analysis in agricultural organic amendments through non-destructive assays using machine learning. PLoS ONE 15(12): e0242821.
  9. Grüner E, Wachendorf M, Astor T (2020) The potential of UAV-borne spectral and textural information for predicting aboveground biomass and N fixation in legume-grass mixtures. PLoS ONE 15(6): e0234703.
  10. Cao Y, Jiang K, Wu J, Yu F, Du W, Xu T (2020) Inversion modeling of japonica rice canopy chlorophyll content with UAV hyperspectral remote sensing. PLoS ONE 15(9): e0238530.
  11. Chebrolu N, Magistri F, Läbe T, Stachniss C (2021) Registration of spatio-temporal point clouds of plants for phenotyping. PLoS ONE 16(2): e0247243.
  12. Jacques CN, Hulbert AK, Westenskow S, Neff MM (2020) Production location of the gelling agent Phytagel has a significant impact on Arabidopsis thaliana seedling phenotypic analysis. PLoS ONE 15(5): e0228515.

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International Day of Women and Girls in Science 2021

Today, 11 February, marks the International Day of Women and Girls in Science. To celebrate, we speak to some recent PLOS ONE authors about their research and their experiences as women in science. Our interviewees study very different aspects of agriculture and food security, but all their work contributes to the development of more efficient and sustainable food systems for the future.

Kirsten Ball (KB)- Postdoctoral Research Associate, Department of Environmental Science, University of Arizona, USA

Author of “High-throughput, image-based phenotyping reveals nutrient-dependent growth facilitation in a grass-legume mixture”

Amaia Albizua (AA)- Associate Professor, Department of Didactics & School Organization, University of the Basque Country, Spain

Author of “Social networks influence farming practices and agrarian sustainability”

Paula Rendón (PR)- PhD Student & Research Assistant, Institute of Physical Geography & Landscape Ecology, University of Hannover, Germany

Author of “Assessment of the relationships between agroecosystem condition and the ecosystem service soil erosion regulation in Northern Germany”

Inderjot Chahal (IC)- Postdoctoral Fellow, School of Environmental Sciences, University of Guelph, Canada

Author of “Cover crop and crop residue removal effects on temporal dynamics of soil carbon and nitrogen in a temperate, humid climate”

Laura Van Eerd (LVE)- Professor, School of Environmental Sciences, University of Guelph, Canada

Author of “Cover crop and crop residue removal effects on temporal dynamics of soil carbon and nitrogen in a temperate, humid climate”

Could you tell us a bit about your research interests and what attracted you to your field of study?

KB: My research is driven from a desire to understand the impacts of agricultural management on soil health, and to increase industry adoption of sustainable production practices. I very much take a plant-soil feedback approach to that goal; I think it is difficult to examine soil health and plant health without considering the interaction between the two.

AA: I am a multidisciplinary scientist studying terrestrial social-ecological systems mitigation and adaptation options to global change. I aim to answer complex sustainability questions such as land use planning accounting for optimizing ecosystem services and social wellbeing under human-driven and environmental crises. I have a special interest in the nexus between land use decision-making processes and the multi-scale connections of land and water governance and other socioeconomic factors.

MI: I have been particularly drawn to research focused on soil fertility and on how it influences crop quality. This is because I believe that soils greatly influence the nutritional quality of all produced food and hence our nutritional well-being. My research on cassava and my work experience on a nutrition project also got me interested in the food and nutrition security of subsistence farming communities in rural parts of Africa.

PR: I am interested in sustainability, resilience and human-nature relationships. Since a very young age, I started to show an interest in environmental issues. But it was later during my studies that I became more aware of the importance of nature in humankind’s survival. I came across the concepts of “ecosystem services” and “ecosystem condition”, and I have been studying them since then.

IC: I study the impacts of sustainable soil management practices on enhancing soil health, soil biogeochemistry (C and N cycling), and crop productivity while minimizing nutrient losses to the environment from vegetable and grain cropping systems. I always had a passion for agriculture, specifically for soil health and fertility. Over the years, I had the pleasure to work and learn from experts in sustainable agriculture, which significantly contributed in strengthening my interest and developing expertise in this area.

What were the key findings of your recent PLOS ONE paper? Why are they interesting and important?

KB: My study used high-throughput, image-based phenotyping (HTP) to distinguish growth patterns, detect facilitation and interpret variations in nutrient uptake in a model mixed-pasture system in response to factorial low and high nitrogen (N) and phosphorus (P) application. HTP has not previously been used to examine pasture species in mixture; it was a useful tool to quantify growth trait variation between contrasting species and to this end is highly useful in understanding nutrient-yield relationships in mixed pasture cultivations.

AA: We found that most farmers were aware of their co-production of nature Contribution to People (NCP) through their land management decisions. We also found that farmers’ awareness about NCP co-production and their land management decisions were correlated with the structure of the social networks among the farming community. Rural network analysis can be useful for understanding the network configuration of rural farming communities to improve rural policy development since it permits understanding interactions between awareness, land management decisions, and knowledge/advice sharing at the landscape level. Considering that those modern farmers’ perceptions and their management practices are significant factors for the creation of the advice network structure, we should incentive structures that make farmers more aware of their contribution to climate regulation to take a more active role within their networks.

MI: In the article, which reports on a research project that I really enjoyed developing and writing up, we showed that cyanogenic glucoside production in cassava is influenced by plant nutritional status, similar to crop yields and well-known crop quality characteristics like fruit colour and taste. Amongst many other things, the study managed to highlight the important role of plant nutritional status (and soil fertility) in producing cassava that is safe to consume for the millions of people that depend on it for their staple food.

PR: We wanted to analyse the relationship between ecosystem condition and services in a regional case study. For this, we used the indicators proposed by the Mapping and Assessment of Ecosystems and their Services (MAES) group of the European Commission to assess the condition of agroecosystems, and compare them against the supply of the ecosystem service erosion control. We identified some correlations between the indicators but also some limitations in the framework, as some indicators cannot explain to what extent ecosystems can provide specific services. These results are interesting because they trigger further research to find better ways to integrate ecosystem condition and services. Additionally, they highlight the need to make temporal and spatially-explicit data available at national and regional scales, that provide more thorough information for policy and decision making.

IC: The key findings of our paper were (a) cover crop adoption in the medium-term (6-yrs) enhanced surface C and N storage in a horticultural cropping system, and (b) cover crop and crop residue retention had an integrative positive effect on increasing soil C and N fractions. This study advanced our understanding of the synergistic effect of cover crop and crop residue retention on the mechanism of soil C and N cycling and increasing soil health in the medium-term.

Photo by Andrea Candraja on Pixabay

What are you working on now?

KB: I am currently working at the University of Arizona on an NRCS arid soil health program for cropping systems. I am prioritizing expanding understanding of what constitutes a ‘healthy’ arid soil, paying particular attention to the interaction of soil organic matter with soil carbonates. If we can describe a soil as healthy, what does that look like for arid systems? Further, if there is an achievable goal for soil health in arid systems, how do we quantify it? I currently have a variety of field trials in cropping systems including forage cropping and viticulture.

AA: I am currently Associate Professor at the University of the Basque Country, but the classes I am performing are quite far from my expertise. The way the system works to get a place at the university here demands you have good research background but also teaching experience and I am now getting such experience. At the same time, I’m collaborating with a colleague at the Autonomous University of Barcelona in a meta-analysis to understand the effectiveness of interventions to adapt to climate change in developing countries.

MI: I recently developed a tool that can be used to assess a subsistence farming community’s vulnerability to cassava cyanide intoxication. The tool is a decision support tool that will help highlight the risk of cassava cyanide intoxication in communities, and will also guide the selection of interventions. Since I had only conducted a pilot study, I am currently planning to have the tool validated using a larger study population.

PR: I am working on a similar study to the one we published in PLOS ONE, but this time at the European scale. We are looking at the condition of agroecosystems and erosion control and the variations of the indicators and their relationships in environmental zones with similar climatic and topographic characteristics.

IC: I am currently working on quantifying soil health and understanding the mechanisms regulating soil C and N dynamics in sustainable cropping systems. I am particularly interested in cover crops, crop rotation, tillage, crop diversification, and fertilizer N management. The major goal of my research is to provide valuable information for developing resilient cropping systems.

What has your experience as a woman in science been like?

KB: I had three female supervisors/mentors throughout graduate school; that representation helped me to build the confidence I needed to know I could succeed. As an early career researcher, a conventional avenue of elevating your position in academia is to align yourself (either in project or manuscript collaboration) with highly established and successful researchers: often white men. Unfortunately, this behavior reinforces and amplifies the underrepresentation of women and BIPOC folk, particularly women of color in STEM. I actively seek non-traditional avenues to create research partners, instead creating respectful, mutual, and equitable working relationships that enhance my knowledge and progression while elevating my peers; namely women of color and early career, female researchers.

AA: My experience has been pretty good but sometimes I have had the feeling of not being heard in the way a man would be. I am very aware of the fact that women tend to hold lower positions, have a less active and visible voice in scientific congresses and in the media and sometimes even charge less (perhaps because we demand less) for the same work. For this reason, I participate in networks that give women visibility into science as well as programs to empower and encourage girls to be scientific. The experience of working previously in Montreal, at McGill University, with a woman as a supervisor and a laboratory group in which most of us were women has been very stimulating and has given me a lot of confidence.

MI: I must say that it is difficult to say whether the challenges I have faced in science have been due to me being a woman or due to me being seen as a younger, less experienced researcher. But both women and younger researchers come up with great ideas and must be given credit, as well as support.

PR: So far, I have had a good experience in science. I found many inspiring women working in my field that have done great work and contributed considerably to science. I have not felt any rejection linked to my background or gender; on the contrary, I feel supported and encouraged by my supervisors and colleagues.

LVE: Fortunately, for 99.2% of the time my gender is inconsequential, as it should be. I could tell you about experiences that would make you wince and would surprise many male scientists. Many people like to think that things are better for the next generation of women in science and that is likely be true, but in my experience sexist, inappropriate comments or micro-aggressions still persist. What has improved, in my opinion, is that many people are better at calling out these behaviours.

Photo by S. Hermann & F. Richter on Pixabay

Has Covid-19 affected your work?

KB: I actually started my postdoc at the UofA from my kitchen bench!! I am mostly meeting people via Zoom, which is lucky because I almost always have pyjama pants on! While I have been able to be very productive working from home (I don’t have any small children to worry about) the social isolation creates a lot of stress. I was lucky enough to fit in some fieldwork at the end of 2020 which should tide me over for a few more months. I also hope to be able to get home and see my family in Australia within the next year, I miss them more than ever at the moment!

AA: Motherhood and Covid-19 have arrived at once so I wouldn’t know how Covid-19 has affected me but motherhood. When you become a mother, it is a year in which producing is done at a high price (physical, mental and emotional). Thanks to my mother’s help I’ve managed to keep publishing and pushing my research but sometimes it’s been really hard. I believe that women scientists who want to be mothers need greater protection so that maternity years are not penalized when it comes to getting scholarships or finding jobs. The first few years, or at least the first year, the time a woman must dedicate to the baby cannot be comparable to that of a man even if we are given the same amount of parental leave.

MI: While writing a research proposal I came to realise that I could not easily design a research project that could be carried out in another country, because of the Covid-19 travel restrictions. Covid-19 has also made within-country movements a challenge; one has to carefully think before planning to conduct a research in a rural area, for fear of carrying the disease there. Drawing up research budgets has also been impossible, as prices keep changing due to the economic disruption.

PR: I have been able to work remotely, so I did not experience a strong interruption in my research. In my institute, we try to keep in touch through informal virtual coffee breaks and weekly meetings. However, I miss the exchange of ideas I had with my supervisor and colleagues in the office. An aspect that I somehow underestimated before is the importance of keeping good mental health. The uncertainty of the situation and having family and friends seriously ill with the virus have taken a toll on my mental health and productivity.

LVE: Yes, like many across the world, my research, teaching and extension work has been greatly impacted. Let me be clear, that I am extremely grateful to be healthy and be employed. I have noticed that the requests for presentations, video and audio interviews have more than doubled, not to mention the additional paperwork. Remote teaching is an onerous time commitment that really limits the opportunities for feedback. I worry about my students well-being and learning experience.  Mostly I miss the meaningful connections within my research team, as well as colleagues and industry partners.

What change do you hope to see in the future of agriculture and food systems?

KB: There needs to be a recognition of the intrinsic connection between plants and soil, and a more holistic management framework that accounts for both. Further, we (white folk) need to recognise how detrimental it is that Indigenous knowledge and motivations of local communities have historically been taken for granted by scientists with a lack of reciprocity in relationships. As agricultural researchers we need to deconstruct historical understanding of agricultural development that ignored native principles of land stewardship, and pledge to seek knowledge from- and develop research programs alongside- indigenous farmers and researchers that recognizes the primacy of native values if we are truly going to look after our productive lands.

AA: I would like to see local, seasonal and respectful production systems. I would like governments to manage markets to regulate global competition.

MI: I would like to see subsistence farming communities able to produce enough nutritious food to feed themselves adequately throughout the year. I would like to see them well-supported with things like good agricultural extension, farming inputs and with access to markets. I feel that while they struggle to feed so many of us, they themselves are left with little as they cannot properly balance household food and income needs.

PR: I would like to see a system of agricultural production that is sustainable in the long term. One that is resilient to future pressures and the impacts of climate change, that considers local knowledge and practices, and that is beneficial for farmers, consumers and the environment.

IC: I hope that future food production becomes environmentally and economically sustainable. I hope the general public becomes more aware of the numerous agroecosystem benefits provided by sustainable land management practices. Growers adopting agricultural practices which enhance agroecosystem resiliency and minimize environmental degradation will be financially compensated. These changes will contribute to developing healthy soils, providing safe and nutritious food to people, and increasing environmental quality. 

LVE: I hope to see a time when the majority of consumers understand considerably more about agriculture and where food comes from. My dream would be an agri-food system where practices that enhance ecosystem services are valued and become the norm. With this knowledge, there could be great advances towards healthy soil, agroecosystems, and people.

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Sustainable cropping systems for the future

As global food demand grows and environmental pressures on agriculture intensify, there is an increasingly urgent need for food systems that are sustainable and resilient. PLOS ONE publishes a range of scientific research touching on all aspects of food systems, from analyses of agronomic efficiency to participatory policy development. Following on from our recent blog on tropical agriculture, here we focus on the integration of agricultural crops in social and economic systems. We highlight a range of recent articles that provide important insights into the structure and function of current cropping systems, and the elaboration and deployment of improved alternatives.

Food system classification and food security metrics

Food systems around the world vary widely in terms of configuration and resilience, and Baer-Nawrocka and Sadowski produced a typology to classify prevalent food systems and levels of food security in individual countries [1]. Their results pinpoint areas of Sub-Saharan Africa and Central Asia where systemic food insecurity is most critical. Whilst the public discourse surrounding food systems often focuses on the quantity of food produced, understanding imbalances in nutritional quality is also of vital importance. In their PLOS ONE article, KC and colleagues compared recommended dietary composition with actual agricultural production [2]. At a global scale, they found evidence for overproduction of grains, fats and sugars, and underproduction of fruits, vegetables and proteins. This led the authors to propose ways of redressing this overall nutritional imbalance without compromising on land use and greenhouse gas emissions. Meanwhile, Grovermann and colleagues assessed eco-efficiency in the food systems of 79 developing countries [3]. They also identified factors that promoted agricultural innovation, finding that the most effective interventions were context-specific. But what factors drive the sustainability of any given food system? This question was addressed by Béné and colleagues, who identified twelve key drivers in a representative set of low-, middle- and high-income countries [4]. They found that most drivers had a negative effect on sustainability and could be associated with the global demographic transition, highlighting the even greater challenges that lie ahead.

Reproducible measures for food (in)security are fundamental to efforts to build a strong evidence base for effective interventions. A key finding of Misselhorn and Hendriks’s systematic review of food insecurity research in South Africa was that there was a widespread lack of consistency in the indicators used to measure food insecurity [5]. They see this as a major limitation for monitoring activities and for developing policies to improve local and regional situations. Meanwhile, working in Brazil and Colombia, Córdoba and colleagues proposed a conceptual and methodological framework for evaluation of resilience in agroecosystems [6]. They used a participatory approach to assess stakeholder agency, which is ranked as an important determinant of overall resilience in their evaluation framework. The need for meaningful measurement of climate resilience spurred Parker and colleagues to develop a climate risk vulnerability assessment for the tropics [7]. They applied their methods in Vietnam, Uganda and Nicaragua, identifying sub-national regions of contrasting vulnerability.

Photo by vandelinodias on Pixabay

Crop diversification

The diversification of agricultural crops is often discussed as a potential route to more resilient food systems, at local, regional and global scales. Research by Smith and colleagues found that six decades of agricultural intensification in India had been associated with increased crop diversity at a national level, although this effect did not occur at a local scale [8]. Looking across a similar time interval, Martin and colleagues compared trends in crop diversity in 22 regions around the world [9]. They found broadly consistent patterns across these regions, including a marked increase in crop diversity in the 1970s-80s but an overall homogenisation of global crop species pools. At the level of the individual farm, the benefits of crop diversification must be weighed against the costs associated with a varied set of management requirements. To explore the potential consequences of labour market shocks on diversified farms, Beal Cohen and colleagues developed a model based on the example of labour-intensive fruit production in Florida [10]. Their results demonstrate that the effects of diversification on farm resilience are highly contingent on wider economic factors, which must be taken into account in agricultural policy development. Other PLOS ONE authors have investigated the potential of specific groups of crops for diversified agriculture. Toensmeier and colleagues focused on perennial vegetables, analysing the existing scientific literature to identify a number of key nutritional and environmental benefits of increased representation of these crops in food systems [11]. There are, however, major structural barriers to crop diversification. To understand these better, Morel and colleagues examined 25 European case-studies, performing a systematic characterisation of the contextual factors influencing the accessibility of crop diversification support schemes [12].

Land use

The land use requirements of agriculture are enormous, and it is crucial for researchers and policymakers to understand how they are affected by external factors and interact with other land uses. Mora and colleagues generated a set of scenarios of how future agricultural land use may be impacted by climate change and a range of socioeconomic factors [13]. These hypothetical scenarios can be used as tools in planning how best to adapt agriculture and food systems to future realities. Meanwhile, Hannah and colleagues examined how climate change may drive a poleward shift in crop cultivation, with extensive ramifications for global ecology and conservation [14]. They found that the expansion of cultivation across these climate-driven agricultural ‘frontiers’ could lead to particularly severe impacts on biodiversity, soil carbon storage and water resources. Debate also continues around perceived potential conflict between land use for edible crops and for bioenergy crops. In their analysis, Henry and colleagues found that, on current trajectories, food and bioenergy production could not be reconciled within a proposed planetary boundary of using 15% of the Earth’s ice-free land surface for crops [15]. Instead, they suggest that significant changes in the demand-side of the food system or revolutionary biotechnologies will be required to achieve such a target.

Photo by flavio10rs on Pixabay

Smallholder agriculture

Smallholder farmers constitute a large proportion of the human population engaged in agricultural production, particularly in the tropics. However, the umbrella term ‘smallholder’ covers a wide variety of different farm types and management strategies. To get a better handle on this diversity, Alvarez and colleagues designed and tested a new classificatory framework for smallholder farming systems in Zambia [16]. Their approach integrated participatory and statistical methods to define a typological basis for future exploration of system innovation and adaptation. Understanding smallholder responses to environmental challenges is a prerequisite for supporting adaptive behaviours. Jaleta and colleagues documented changes in management practices taken by Ethiopian smallholders in the wake of the 2010/11 wheat rust epidemic [17]. Accessibility of improved wheat seed sources was a key factor in determining the strategy taken by individual farmers, an insight which could inform future attempts to promote more resilient behaviours. Meanwhile, working in Tanzania, Steinke and colleagues tested a methodological approach to identifying the practices underpinning unusually high levels of agricultural and economic success in smallholder households [18]. They found 14 practices that could be formulated as recommendations or support schemes for other households to improve their production and resilience.

Similarly, understanding the factors that influence whether smallholders adopt agricultural intensification or diversification practices is a crucial part of efforts to remove barriers to more resilient farm management. Chen and colleagues analysed data from 15 countries, finding that many drivers of the adoption of intensification were common across countries and regions [19]. By contrast, most drivers of the adoption of diversification were specific to local contexts. It is by no means the case that all smallholders are subsistence farmers. Sibhatu and Qaim found that many Ethiopian smallholders are dependent on access to local markets to purchase 42% of their household calorie consumption [20]. Market-purchased foods were especially important for dietary quality and diversity, and the authors argue that this shows the need for policies that ensure that such markets are reliably accessible.

Photo by redfam on Pixabay

Climate adaptation

As climate change intensifies, adaptation of food systems becomes ever more urgent. The suitability of individual crop species for novel climates will require continuous reassessment, but projections such as those of Chemura and colleagues provide crucial insights into likely trends in crop productivity [21]. They found that different crop species in Ghana are likely to respond very differently to changes in climatic conditions, with important implications for where they are grown and how they are managed. De Pinto and colleagues have explored how climate smart agriculture measures could have a positive impact, but stressed the need for sufficient investment and coordination across the sector [22]. Working on a similar theme, Lan and colleagues identified factors including income inequality and profitability and affordability of CSA practices that affect adoption [23]. The impacts of increased climate variability and extreme events are likely to be particularly keenly felt at the level of individual farmers. In their analysis of smallholder household surveys from 15 countries in Latin America, Africa and South Asia, Niles and Salerno found that climate shocks were already common experiences [24]. They advocated for a renewed focus on building resilience and adaptive capacity in policy measures specifically designed to support smallholders.

Research into food systems is necessarily diverse and interdisciplinary, extending to many other issues not covered here such as food storage and distribution. PLOS ONE provides a venue for articles spanning all aspects of this vital subject. Dive in to find more!


  1. Baer-Nawrocka A, Sadowski A (2019) Food security and food self-sufficiency around the world: A typology of countries. PLoS ONE 14(3): e0213448.
  2. KC KB, Dias GM, Veeramani A, Swanton CJ, Fraser D, Steinke D, et al. (2018) When too much isn’t enough: Does current food production meet global nutritional needs? PLoS ONE 13(10): e0205683.
  3. Grovermann C, Wossen T, Muller A, Nichterlein K (2019) Eco-efficiency and agricultural innovation systems in developing countries: Evidence from macro-level analysis. PLoS ONE 14(4): e0214115.
  4. Béné C, Fanzo J, Prager SD, Achicanoy HA, Mapes BR, Alvarez Toro P, et al. (2020) Global drivers of food system (un)sustainability: A multi-country correlation analysis. PLoS ONE 15(4): e0231071.
  5. Misselhorn A, Hendriks SL (2017) A systematic review of sub-national food insecurity research in South Africa: Missed opportunities for policy insights. PLoS ONE 12(8): e0182399.
  6. Córdoba C, Triviño C, Toro Calderón J (2020) Agroecosystem resilience. A conceptual and methodological framework for evaluation. PLoS ONE 15(4): e0220349.
  7. Parker L, Bourgoin C, Martinez-Valle A, Läderach P (2019) Vulnerability of the agricultural sector to climate change: The development of a pan-tropical Climate Risk Vulnerability Assessment to inform sub-national decision making. PLoS ONE 14(3): e0213641.
  8. Smith JC, Ghosh A, Hijmans RJ (2019) Agricultural intensification was associated with crop diversification in India (1947-2014). PLoS ONE 14(12): e0225555.
  9. Martin AR, Cadotte MW, Isaac ME, Milla R, Vile D, Violle C (2019) Regional and global shifts in crop diversity through the Anthropocene. PLoS ONE 14(2): e0209788.
  10. Beal Cohen AA, Judge J, Muneepeerakul R, Rangarajan A, Guan Z (2020) A model of crop diversification under labor shocks. PLoS ONE 15(3): e0229774.
  11. Toensmeier E, Ferguson R, Mehra M (2020) Perennial vegetables: A neglected resource for biodiversity, carbon sequestration, and nutrition. PLoS ONE 15(7): e0234611.
  12. Morel K, Revoyron E, San Cristobal M, Baret PV (2020) Innovating within or outside dominant food systems? Different challenges for contrasting crop diversification strategies in Europe. PLoS ONE 15(3): e0229910.
  13. Mora O, Le Mouël C, de Lattre-Gasquet M, Donnars C, Dumas P, Réchauchère O, et al. (2020) Exploring the future of land use and food security: A new set of global scenarios. PLoS ONE 15(7): e0235597.
  14. Hannah L, Roehrdanz PR, K. C. KB, Fraser EDG, Donatti CI, Saenz L, et al. (2020) The environmental consequences of climate-driven agricultural frontiers. PLoS ONE 15(2): e0228305.
  15. Henry RC, Engström K, Olin S, Alexander P, Arneth A, Rounsevell MDA (2018) Food supply and bioenergy production within the global cropland planetary boundary. PLoS ONE 13(3): e0194695.
  16. Alvarez S, Timler CJ, Michalscheck M, Paas W, Descheemaeker K, Tittonell P, et al. (2018) Capturing farm diversity with hypothesis-based typologies: An innovative methodological framework for farming system typology development. PLoS ONE 13(5): e0194757.
  17. Jaleta M, Hodson D, Abeyo B, Yirga C, Erenstein O (2019) Smallholders’ coping mechanisms with wheat rust epidemics: Lessons from Ethiopia. PLoS ONE 14(7): e0219327.
  18. Steinke J, Mgimiloko MG, Graef F, Hammond J, van Wijk MT, van Etten J (2019) Prioritizing options for multi-objective agricultural development through the Positive Deviance approach. PLoS ONE 14(2): e0212926.
  19. Chen M, Wichmann B, Luckert M, Winowiecki L, Förch W, Läderach P (2018) Diversification and intensification of agricultural adaptation from global to local scales. PLoS ONE 13(5): e0196392.
  20. Sibhatu KT, Qaim M (2017) Rural food security, subsistence agriculture, and seasonality. PLoS ONE 12(10): e0186406.
  21. Chemura A, Schauberger B, Gornott C (2020) Impacts of climate change on agro-climatic suitability of major food crops in Ghana. PLoS ONE 15(6): e0229881.
  22. De Pinto A, Cenacchi N, Kwon H-Y, Koo J, Dunston S (2020) Climate smart agriculture and global food-crop production. PLoS ONE 15(4): e0231764.
  23. Lan L, Sain G, Czaplicki S, Guerten N, Shikuku KM, Grosjean G, et al. (2018) Farm-level and community aggregate economic impacts of adopting climate smart agricultural practices in three mega environments. PLoS ONE 13(11): e0207700.
  24. Niles MT, Salerno JD (2018) A cross-country analysis of climate shocks and smallholder food insecurity. PLoS ONE 13(2): e0192928.

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Growing together– celebrating tropical agriculture research in PLOS ONE

Agricultural production sustains human life across the globe, but nowhere does it face a more complex combination of socioeconomic and environmental constraints- or play a more central role in supporting livelihoods- than in the world’s tropical regions. In-country expertise and research capacity are expanding, and there is increasing recognition of the importance both of valuing local knowledge and sharing findings widely. Tropical agricultural research is therefore entering an exciting era- and the stakes are high. Climate change, emerging pests and diseases, and growing demand for food are just a few of the intense and mounting pressures on crop production. But right across the tropics, researchers are rising to the challenge. Here, we shine a spotlight on some recent PLOS ONE articles representative of the innovative agricultural research taking place in tropical countries and driving forwards the development of sustainable, resilient cropping systems.

Land management

Appropriate land management practices are at the heart of sustainable agriculture. Developing such practices requires a clear understanding of the relationships between soil properties and crop performance. One important focus of research is the effect of soil nutrient status on both growth and the production of secondary metabolites. For example, cassava can accumulate toxic cyanide when grown in nutrient-deficient soils, and Imakumbili and colleagues found that this explained the occurrence of neurological conditions in human populations in areas of Tanzania [1]. It is also vital to understand how plants react to fluctuations in soil water content, such as through modification of root architecture, as studied using modelling approaches in pearl millet in Senegal by Faye and colleagues [2]. Since the soil itself is of course the basis of all terrestrial crop production, accurate spatial mapping of soil properties can play a crucial role in planning crop deployment across complex landscapes. We have recently published examples of cutting-edge soil mapping projects from countries including Burkina Faso [3] and Ethiopia [4], based on a variety of techniques and with applications in sustainable agronomic practice.

Crop diseases

Disease is a major challenge for tropical agriculture, with climatic conditions often being highly conducive to pathogen development and propagation. Monitoring programmes can help track endemic disease patterns as well as identifying dramatic long-distance dispersal events, such as the highly concerning arrival of wheat blast fungus in Zambia, recently reported in PLOS ONE [5]. Modelling can also be used to explore the potential distribution and severity of diseases across geographical regions, as with the banana diseases black sigatoka [6] and fusarium wilt [7]. Of course, understanding pathogen biology is also of fundamental importance, from pathological mechanisms to genetic diversity, which was the focus of Abidin and colleagues’ study of jackfruit bronzing disease [8]. These authors found evidence for a high level of genetic uniformity in strains from across Malaysia, a result which will inform future surveillance and management strategies. Beyond the biological detail of host-disease interactions, research also focuses on modelling the impact of the disease on yield and production efficiency, as studied by Cerda and co-authors in the context of Costa Rican coffee [9].

Photo by Skitterphoto on Pixabay

Diverse crops and genes

Getting to grips with the diversity and structure in the germplasm of crops is key to unlocking their full potential. PLOS ONE has recently published important analyses of genetic diversity in tropical crops ranging from maize [10, 11] and cassava [12] to banana [13], yam [14], and sweet potato [15]. These studies lay the groundwork for future crop improvement, as examined in the case of rice by Ali and colleagues [16]. They described a breeding procedure with potential for improving rice plant tolerance to multiple environmental stresses. It is also widely recognised that more research is needed on the less well studied or ‘neglected’ crops in addition to the familiar staples that have traditionally attracted the vast majority of research funding. Neglected crops have enormous potential on many levels, as was recently highlighted in the case of Bambara groundnut in Zimbabwe by Mubaiwa and co-authors [17]. They showed that more widespread adoption of this crop could confer significant benefits in terms of both nutrition and agricultural resilience.

Agroecological systems

Many tropical crops are cultivated in agroecological or agroforestry systems, where crops are grown in mixture with each other and with trees that provide a range of ecosystem services. These production systems are sometimes the product of long-established traditional practice, and other times the result of recent innovation. The scientific evidence base around these systems is ever-growing; recent articles in PLOS ONE cover the roles played by shade trees in plantations of cocoa in Ghana [18, 19] coffee in China [20], and banana in Guadeloupe [21].  Elsewhere, relationships between agroecological management of coffee plantations and mycorrhizal fungi diversity was studied by Prates Júnior and colleagues in Brazil [22]. They found that mycorrhizal diversity in agroecological plantations was significantly higher than in conventionally-managed plantations, and similar to in natural forest.

Climate change

All tropical agriculture, whatever the crop or the location, will be impacted by climate change. Forecasts of the likely consequences of altered growing conditions on the viability of cropping patterns are an important tool to anticipate the need for agronomic adaptation, as in the case of a study by Duku and colleagues in Benin [23]. They found that between 50% and 95% of cultivated areas in the Upper Ouémé watershed that currently support rainfed sequential cropping will be forced to revert to single cropping due to climate change. Models are also developed- using mechanistic or correlative approaches- to inform adaptation strategies for specific crops, as with cocoa in Brazil [24] and rice in the Philippines [25].

Photo by torricojc on Pixabay

Technological solutions

In the 21st century, tropical agricultural research is characterised by creative innovation, spurred by the many challenges of our times. New technological solutions for particular agronomic problems are reported frequently, as in the recent case of a spectroscopic tool for identification of barley, chickpea and sorghum cultivars in Ethiopia [26]. The authors of this study also produced an accompanying R package for cultivar identification based on spectral data. Another consequence of the growing availability of communications technology among rural populations in the tropics is that it provides new opportunities for distributed research using citizen science methodologies, as studied by Beza and colleagues in Honduras, Ethiopia and India [27]. They provide insights into the potential of technologically-enabled citizen science in tropical agriculture research, and identify ways of reducing barriers to participation.

Socioeconomic factors

Agricultural production does not take place in a vacuum. PLOS ONE has published a wide variety of research that addresses the socioeconomic contexts of tropical agricultural systems. For example, Volsi and colleagues have explored the dynamics of coffee production in Brazil in relation to policy environments and market forces [28], while Effendy and co-authors have looked at the factors driving the economic efficiency of cocoa production in Indonesia [29]. Research elsewhere has examined the effects of the adoption of new cash crops for export on household food security and wellbeing and agroecological resilience, including in Guatemala [30] and Laos [31].

Looking ahead

What directions will be explored in future tropical agriculture research? At one level, priorities for major research programmes are likely to be developed by national and supra-national institutes in the tropics, whose voices are taking their place on the global stage. However, there is recognition that research efforts should also be guided by the priorities of stakeholders at a regional and local level. This can involve direct consultation with farmers and regional experts, or quantitative modelling of priorities from multiple inputs, as in the study undertaken by Alene and colleagues in the context of cassava production in Africa, Asia and Latin America [32]. Multi-stakeholder platforms (MSPs) have demonstrated great potential as vehicles for collaborative identification of research priorities and opportunities for innovation, though as highlighted in a social network study by Hermans and colleagues based in Burundi, Rwanda and the Democratic Republic of Congo, MSPs must be carefully orchestrated to achieve maximal connectivity and exchange of ideas and expertise [33].

PLOS ONE is a global community. We are proud to provide a venue for research on all aspects of tropical agricultural systems, including interdisciplinary work, new methods and technologies, and to make these findings freely available to all.


  1. Imakumbili MLE, Semu E, Semoka JMR, Abass A, Mkamilo G (2019) Soil nutrient adequacy for optimal cassava growth, implications on cyanogenic glucoside production: A case of konzo-affected Mtwara region, Tanzania. PLoS ONE 14(5): e0216708.
  2. Faye A, Sine B, Chopart J-L, Grondin A, Lucas M, Diedhiou AG, et al. (2019) Development of a model estimating root length density from root impacts on a soil profile in pearl millet (Pennisetum glaucum (L.) R. Br). Application to measure root system response to water stress in field conditions. PLoS ONE 14(7): e0214182.
  3. Forkuor G, Hounkpatin OKL, Welp G, Thiel M (2017) High Resolution Mapping of Soil Properties Using Remote Sensing Variables in South-Western Burkina Faso: A Comparison of Machine Learning and Multiple Linear Regression Models. PLoS ONE 12(1): e0170478.
  4. Nyssen J, Tielens S, Gebreyohannes T, Araya T, Teka K, Van de Wauw J, et al. (2019) Understanding spatial patterns of soils for sustainable agriculture in northern Ethiopia’s tropical mountains. PLoS ONE 14(10): e0224041.
  5. Tembo B, Mulenga RM, Sichilima S, M’siska KK, Mwale M, Chikoti PC, et al. (2020) Detection and characterization of fungus (Magnaporthe oryzae pathotype Triticum) causing wheat blast disease on rain-fed grown wheat (Triticum aestivum L.) in Zambia. PLoS ONE 15(9): e0238724.
  6. Yonow T, Ramirez-Villegas J, Abadie C, Darnell RE, Ota N, Kriticos DJ (2019) Black Sigatoka in bananas: Ecoclimatic suitability and disease pressure assessments. PLoS ONE 14(8): e0220601.
  7. Mostert D, Molina AB, Daniells J, Fourie G, Hermanto C, Chao C-P, et al. (2017) The distribution and host range of the banana Fusarium wilt fungus, Fusarium oxysporum f. sp. cubense, in Asia. PLoS ONE 12(7): e0181630.
  8. Abidin N, Ismail SI, Vadamalai G, Yusof MT, Hakiman M, Karam DS, et al. (2020) Genetic diversity of Pantoea stewartii subspecies stewartii causing jackfruit-bronzing disease in Malaysia. PLoS ONE 15(6): e0234350.
  9. Cerda R, Avelino J, Gary C, Tixier P, Lechevallier E, Allinne C (2017) Primary and Secondary Yield Losses Caused by Pests and Diseases: Assessment and Modeling in Coffee. PLoS ONE 12(1): e0169133.
  10. Boakyewaa Adu G, Badu-Apraku B, Akromah R, Garcia-Oliveira AL, Awuku FJ, Gedil M (2019) Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers. PLoS ONE 14(4): e0214810.
  11. Bedoya CA, Dreisigacker S, Hearne S, Franco J, Mir C, Prasanna BM, et al. (2017) Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. PLoS ONE 12(4): e0173488.
  12. Ferguson ME, Shah T, Kulakow P, Ceballos H (2019) A global overview of cassava genetic diversity. PLoS ONE 14(11): e0224763.
  13. Nyine M, Uwimana B, Swennen R, Batte M, Brown A, Christelová P, et al. (2017) Trait variation and genetic diversity in a banana genomic selection training population. PLoS ONE 12(6): e0178734.
  14. Arnau G, Bhattacharjee R, MN S, Chair H, Malapa R, Lebot V, et al. (2017) Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers. PLoS ONE 12(3): e0174150.
  15. Glato K, Aidam A, Kane NA, Bassirou D, Couderc M, Zekraoui L, et al. (2017) Structure of sweet potato (Ipomoea batatas) diversity in West Africa covaries with a climatic gradient. PLoS ONE 12(5): e0177697.
  16. Ali J, Xu J-L, Gao Y-M, Ma X-F, Meng L-J, Wang Y, et al. (2017) Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.). PLoS ONE 12(3): e0172515.
  17. Mubaiwa J, Fogliano V, Chidewe C, Bakker EJ, Linnemann AR (2018) Utilization of bambara groundnut (Vigna subterranea (L.) Verdc.) for sustainable food and nutrition security in semi-arid regions of Zimbabwe. PLoS ONE 13(10): e0204817.
  18. Asigbaase M, Sjogersten S, Lomax BH, Dawoe E (2019) Tree diversity and its ecological importance value in organic and conventional cocoa agroforests in Ghana. PLoS ONE 14(1): e0210557.
  19. Abdulai I, Jassogne L, Graefe S, Asare R, Van Asten P, Läderach P, et al. (2018) Characterization of cocoa production, income diversification and shade tree management along a climate gradient in Ghana. PLoS ONE 13(4): e0195777.
  20. Rigal C, Vaast P, Xu J (2018) Using farmers’ local knowledge of tree provision of ecosystem services to strengthen the emergence of coffee-agroforestry landscapes in southwest China. PLoS ONE 13(9): e0204046.
  21. Tardy F, Damour G, Dorel M, Moreau D (2017) Trait-based characterisation of soil exploitation strategies of banana, weeds and cover plant species. PLoS ONE 12(3): e0173066.
  22. Prates Júnior P, Moreira BC, da Silva MdCS, Veloso TGR, Stürmer SL, Fernandes RBA, et al. (2019) Agroecological coffee management increases arbuscular mycorrhizal fungi diversity. PLoS ONE 14(1): e0209093.
  23. Duku C, Zwart SJ, Hein L (2018) Impacts of climate change on cropping patterns in a tropical, sub-humid watershed. PLoS ONE 13(3): e0192642.
  24. Gateau-Rey L, Tanner EVJ, Rapidel B, Marelli J-P, Royaert S (2018) Climate change could threaten cocoa production: Effects of 2015-16 El Niño-related drought on cocoa agroforests in Bahia, Brazil. PLoS ONE 13(7): e0200454.
  25. Stuecker MF, Tigchelaar M, Kantar MB (2018) Climate variability impacts on rice production in the Philippines. PLoS ONE 13(8): e0201426.
  26. Kosmowski F, Worku T (2018) Evaluation of a miniaturized NIR spectrometer for cultivar identification: The case of barley, chickpea and sorghum in Ethiopia. PLoS ONE 13(3): e0193620.
  27. Beza E, Steinke J, van Etten J, Reidsma P, Fadda C, Mittra S, et al. (2017) What are the prospects for citizen science in agriculture? Evidence from three continents on motivation and mobile telephone use of resource-poor farmers. PLoS ONE 12(5): e0175700.
  28. Volsi B, Telles TS, Caldarelli CE, Camara MRGd (2019) The dynamics of coffee production in Brazil. PLoS ONE 14(7): e0219742.
  29. Effendy, Pratama MF, Rauf RA, Antara M, Basir-Cyio M, Mahfudz, et al. (2019) Factors influencing the efficiency of cocoa farms: A study to increase income in rural Indonesia. PLoS ONE 14(4): e0214569.
  30. Méthot J, Bennett EM (2018) Reconsidering non-traditional export agriculture and household food security: A case study in rural Guatemala. PLoS ONE 13(5): e0198113.
  31. Thanichanon P, Schmidt-Vogt D, Epprecht M, Heinimann A, Wiesmann U (2018) Balancing cash and food: The impacts of agrarian change on rural land use and wellbeing in Northern Laos. PLoS ONE 13(12): e0209166.
  32. Alene AD, Abdoulaye T, Rusike J, Labarta R, Creamer B, del Río M, et al. (2018) Identifying crop research priorities based on potential economic and poverty reduction impacts: The case of cassava in Africa, Asia, and Latin America. PLoS ONE 13(8): e0201803.
  33. Hermans F, Sartas M, van Schagen B, van Asten P, Schut M (2017) Social network analysis of multi-stakeholder platforms in agricultural research for development: Opportunities and constraints for innovation and scaling. PLoS ONE 12(2): e0169634.

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Introducing the Microbial Ecology of Changing Environments Collection

We are very pleased to be launching our Microbial Ecology in Changing Environments Collection, the product of a call for papers convened by PLOS ONE and our Guest Editors, Melissa Cregger and Stephanie Kivlin. The research in the Collection crosses disciplinary boundaries and represents a wide range of geographies, providing a snapshot of the diversity of research in contemporary microbial ecology. More articles will be added in due course, so please check back for updates!

Several articles highlighted in the Collection address the structure and dynamics of microbial communities in marine or aquatic environments. Three North American studies feature in the initial set of articles. Working in the Southern Californian Bight, Larkin and colleagues explored the effect of El Niño events on cyanobacterial populations [1]. Meanwhile, Vogel and colleagues found evidence for environmental and host-specific influences on microbial community structure on seagrass off the coast of Florida [2]. Finally, using a wetland mesocosm in Connecticut, Donato and co-workers performed an integrative study of microbial and plant responses to simulated chemical pollution [3].

The impact of natural disturbance on microbial communities was another theme that emerged in submissions to the Collection. In this first batch of articles, this is represented by the work of Eaton and colleagues, who examined how a major hurricane affected soil microbes in primary forests in Costa Rica [4].

The microbial ecology of manmade environments also features in the Collection. Maguvu and co-workers analysed the microbiome and physicochemical properties of drinking water production plants in South Africa, identifying significant variation in microbial community structure between facilities [5].

Last but not least, the Collection includes new research on the relationships between microbial communities living in dynamic environments within host organisms. Working in the UK, Garber and colleagues examined the effect of abrupt dietary changes in ponies on gut microbiota, with important implications for animal management [6].

The research in the Collection provides valuable insights into the mechanisms and consequences of microbial interactions with dynamic environments, and highlights the broad range of systems in which scientists are actively engaged in elucidating these phenomena.


  1. Larkin AA, Moreno AR, Fagan AJ, Fowlds A, Ruiz A, Martiny AC (2020) Persistent El Niño driven shifts in marine cyanobacteria populations. PLoS ONE 15(9): e0238405.
  2. Vogel MA, Mason OU, Miller TE (2020) Host and environmental determinants of microbial community structure in the marine phyllosphere. PLoS ONE 15(7): e0235441.
  3. Donato M, Johnson O, Steven B, Lawrence BA (2020) Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses. PLoS ONE 15(7): e0235225.
  4. Eaton WD, McGee KM, Alderfer K, Jimenez AR, Hajibabaei M (2020) Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica. PLoS ONE 15(7): e0231187.
  5. Maguvu TE, Bezuidenhout CC, Kritzinger R, Tsholo K, Plaatjie M, Molale-Tom LG, et al. (2020) Combining physicochemical properties and microbiome data to evaluate the water quality of South African drinking water production plants. PLoS ONE 15(8): e0237335.
  6. Garber A, Hastie P, McGuinness D, Malarange P, Murray J-A (2020) Abrupt dietary changes between grass and hay alter faecal microbiota of ponies. PLoS ONE 15(8): e0237869.

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Taking a walk on the wild side: An interview with the Guest Editors of our Rewilding & Restoration Call for Papers

PLOS ONE has an open Call for Papers on Rewilding & Restoration, with selected submissions to be featured in an upcoming Collection. We hope to feature a diverse range of multidisciplinary and interdiscipinary research, and are especially keen to encourage studies from ecoregions and voices that are underrepresented in the restoration literature. 

We asked three of the Guest Editors- Karen Holl, Benis Egoh, and Chris Sandom- to share their thoughts on the past, present, and future of research in rewilding and ecological restoration.

Why is rewilding and restoration an important area of research? How is it relevant to contemporary society and the challenges we face?

KH: Over the past few years there have been a growing number of commitments at the global, national and regional scale to restore ecosystems to conserve biodiversity, sequester carbon, improve water quality and supply, and provide goods and services to people. For example, the United Nations has declared 2021-2030 the Decade on Ecosystem Restoration and the Bonn Challenge aims to get countries to commit to restore 350 million hectares of forest (an area roughly the size of India) by 2030. So there is a dramatic need for ecological and social studies of how to successfully scale up restoration to the large areas proposed.

BE: Restoration is important because it is the only means through which we can recover nature that has been lost. However, it is important that we understand what, how and where we want to restore. One of the biggest challenges is how to measures restoration success. In my opinion, many times we set out to restore with an objective in mind without thinking of the trade-offs and how to measure our success.

CS: We are about to enter the UN’s Decade on Ecosystem Restoration (2021-2030). It has been declared to ‘massively scale up the restoration of degraded and destroyed ecosystems’ to help ‘fight the climate crisis and enhance food security, water supply and biodiversity’. It is an exciting prospect! But, there is a danger this decade will be squandered if restoration practice is not combined with effective rewilding and restoration research. We need this science to improve our understanding of how to increase the probability of rewilding and restoration success across different ecosystems and circumstances. If we can do the science right, we will make restoration more effective and efficient, meaning limited resources can be put to the greatest use in our efforts to meet the big sustainability challenges.

How does your own research fit into this theme?

KH: For the past 25 years, I have studied how to restore forests, primarily in Latin America, and a range of ecosystems in California and worked with practitioners on how to implement the results of this work. I hope that the papers in this Collection will provide additional insights and case studies that complement my recent Primer of Ecological Restoration book and that I can use in teaching.

BE: In my research, I investigate the trade-offs and benefits from restoration and how we can plan to minimise these trade-offs- where should we be restoring to get the biggest benefits while minimizing cost?

CS: My research is focused on rewilding, in particular, trophic rewilding. I want to understand how reintroducing large mammals can help ecosystems restore and maintain themselves. I typically look at how carnivores influence herbivores, herbivores influence vegetation structure, and how this effects ecosystem functioning and the delivery of ecosystem services like mitigating climate change. I do my best to cover multiple spatial and temporal scales, covering local field projects, such as the Knepp rewilding project, to global macroecological research and looking at snapshot comparisons in the present to palaeoecology that spans millennia.

What trends or exciting advances have you seen in your field recently?

KH: There is increasing recognition of the importance of socioeconomic considerations. The scale of studies is also slowly increasing, which is important. There is increasing recognition that we are restoring in a time of rapid global change and that our restoration approaches need to reflect this reality.

BE: The most exciting advances to me is the research around financing restoration and how a variety of sectors including insurance companies are coming on board to fund restoration measures. Beneficiaries of restoration projects are starting to understand the benefit they get from nature through research on ecosystem services. Also, our research on planning restoration to achieve multiple benefits moves away from traditional ad-hoc restoration. However, implementation of restoration plans is still very low because restoration is mostly opportunistic.

CS: Two papers I’ve really enjoyed this year are “The megabiota are disproportionately important for biosphere functioning” by Brian Enquist and colleagues and “Trophic rewilding revives biotic resistance to shrub invasion” (paywall) by Jennifer Guyton and colleagues. The first provides a theoretical underpinning for the importance of ‘megabiota’ – the largest plants and animals – for driving biosphere scale processes like ecosystem total biomass, resource flows and fertility using metabolic scaling theory. The second reports that in Gorongosa National Park, Mozambique, a decade of large ungulate population recovery has reversed the expansion of an invasive woody species, which had established after the megafauna had been massively reduced in the preceding decades. I think these papers offer important advances in the theory and empirical evidence supporting trophic rewilding.

How does interdisciplinarity contribute to progress in this area of research?

KH: Restoration ecology is an inherently interdisciplinary field. Even if we knew everything about the science of the physical and ecological processes needed to restore ecosystems, which we don’t, success of ecological restoration projects depends critically on engaging stakeholders throughout the process, from planning to implementation to maintenance and monitoring. We need good examples of projects that have succeeded in addressing legal, economic, and social considerations to result in ecological restoration projects that last beyond the first few years.

BE: Successful restoration requires information on land suitability from soil scientists, cost of restoration from an economic perspective, type of species and habitat requirement from ecologists, consideration of the social aspect and careful planning to maximize benefits. Interdisciplinarity is therefore at the center of research in restoration.

CS: Interdisciplinary research is absolutely essential in rewilding and restoration. While the practices of rewilding and restoration seem to be focused on ecology, the factors governing success or failure are typically more about people. As a result, we need social scientists, psychologists, economists, researchers across the humanities as well as practitioners and indigenous and local knowledge to develop and implement innovative rewilding and restoration science.

What advice would you give to a student keen to work in this area of research?

KH: I tell my students to get training in both the natural and social sciences. It is important thing to get hands on experience working on restoration projects to understand the constraints and opportunities of on-the-ground projects and to collaborate with practitioners on designing research questions that are both scientifically rigorous and will help improve restoration efforts.

BE: This is an exciting area of research with a variety of directions that can be pursued.

CS: Think big and get creative. Rewilding and restoration are systems science. They are all about understanding how all the parts of nature, including people, fit together and function. You need to think about the system as a whole, and how whatever it is you are researching fits into that bigger picture. You need to address the question: what are the potential cascading effects of any particular rewilding or restoration action? Because nature is a complex system it is dynamic and chaotic, so you need to be comfortable with uncertainty and work in probabilities. Also, we still have a lot to learn so get creative and embrace diversity in thinking and practice. It is an exciting and challenging field to work in, it makes it very rewarding!

The post Taking a walk on the wild side: An interview with the Guest Editors of our Rewilding & Restoration Call for Papers appeared first on EveryONE.

Maximizing the rigor and reproducibility of citizen science in ecological research

PLOS ONE is organizing a Twitter chat on citizen science methodologies on 2nd April- see details below

Citizen science (CS) encompasses a broad range of research methodologies that involve public participation for data collection, transcription or analysis. Applications of CS have been found in many disciplines, but ecology has consistently been at the forefront. While some CS-based ecological monitoring schemes- such as the UK Butterfly Monitoring Scheme, established in 1976- have been running for decades, the popularity of CS has grown rapidly in more recent years. A wide range of projects based on CS methodologies are now being undertaken around the world, at local, national and international scales. The value of volunteer participation in activities ranging from transect-based species monitoring (Wepprich et al., 2019) and collection of biological specimens for lab-based analysis (Larson et al., 2020; Rasmussen et al., 2020) to crowdsourcing of creative thinking for study design (Can et al., 2017), has been repeatedly demonstrated.  Studies have also highlighted the particular utility of CS methodologies in supporting long-term ecological monitoring in resource-limited contexts, including in economically developing countries (Gouraguine et al., 2019). Meanwhile, examples of the real-world impact of CS research are abundant, both in specific ecological interventions and the wider political discourse. For instance, the influential UK State of Nature 2019 report, likely to be a key source of evidence for future environmental legislation, cites the outcomes of a wealth of CS projects.

With the expansion of CS research, there is lively debate about how to maximise rigor and reproducibility in different types of CS methodologies. One of the crucial aspects of a successful CS study is an appropriately designed protocol, which features a realistic degree of complexity and accounts for the specific challenges of handling CS-derived data. An example of this is provided by a recent comprehensive report of the design, launch and assessment of the UK National Plant Monitoring Scheme (Pescott et al., 2019). Pre-testing of protocols prior to project launch can provide confidence in the robustness of the study design. When designing a CS study, it is also important to understand volunteer motivation and ensure that this is appropriately matched with the nature of the task to be performed (Lyons & Zhang, 2019). Some CS studies utilize narrower demographic groups to meet the required level of motivation and understanding, such as amateur naturalists (Hallmann et al., 2017) or students who are following a course in a related topic (Chiovitti et al., 2019). Depending on the type of study, researchers may also plan to support CS volunteers with training or technological aids, increasingly in the form of mobile apps (Ožana et al., 2019; Appenfeller et al., 2020).



A certain amount of error, either random or systematic, is likely to be introduced by the collection of data by CS volunteers, and study designs must account for this. The level of error can be reduced by allowing volunteers to provide clarifying metadata or to register uncertainty (Torre et al., 2019), or using incentives to reduce sampling bias (Callaghan et al., 2019), but researchers should also ensure that they have means to assess the accuracy of contributed data (Falk et al., 2019; Gibson et al., 2019). Much ecological research is based on large public databases of volunteer-contributed records of species distributions, phenological events and other observational data (e.g. Siljamo et al., 2020). There is an active discussion in the ecological research community about how to maximize the reliability and utility of such data (Ball-Damerow et al., 2019).

The particular considerations that have to be made in the design, execution and evaluation of CS studies has led to calls for dedicated standards and guidelines for CS research. Of course, any such tools must strike the balance between promoting appropriate levels of standardization and allowing the flexibility required for applications of CS methodologies across diverse settings and research questions. Whilst some progress has been made towards this goal, maintaining an open and constructive dialogue among CS practitioners and other stakeholders remains critical to ensure that researchers, volunteers and society are able to realize the full potential of CS.

To foster discussion of these important issues, PLOS ONE (@plosone) will be moderating a Twitter chat on citizen science methodologies on Thursday 2nd April starting at 4pm BST (8am PDT, 11am EDT, 5pm CET). This is a chance for the CS community to share perspectives, experiences and suggestions for best practice. We’ll aim to cover the following questions (and more!):

  • How far can methods in CS projects be standardized?
  • What steps should be taken to maximize CS data quality?
  • Is there a need for clearer guidelines for the design and execution of CS studies?
  • How should credit for data collection be apportioned?

You can take part by using the hashtag #citscichat– we hope to see you there!



Appenfeller LR, Lloyd S, Szendrei Z (2020) Citizen science improves our understanding of the impact of soil management on wild pollinator abundance in agroecosystems. PLoS ONE 15(3): e0230007.

Ball-Damerow JE, Brenskelle L, Barve N, Soltis PS, Sierwald P, Bieler R, et al. (2019) Research applications of primary biodiversity databases in the digital age. PLoS ONE 14(9): e0215794.

Callaghan CT, Rowley JJL, Cornwell WK, Poore AGB, Major RE (2019) Improving big citizen science data: Moving beyond haphazard sampling. PLoS Biol 17(6): e3000357.

Can ÖE, D’Cruze N, Balaskas M, Macdonald DW (2017) Scientific crowdsourcing in wildlife research and conservation: Tigers (Panthera tigris) as a case study. PLoS Biol 15(3): e2001001.

Chiovitti A, Thorpe F, Gorman C, Cuxson JL, Robevska G, Szwed C, et al. (2019) A citizen science model for implementing statewide educational DNA barcoding. PLoS ONE 14(1): e0208604.

Falk S, Foster G, Comont R, Conroy J, Bostock H, Salisbury A, et al. (2019) Evaluating the ability of citizen scientists to identify bumblebee (Bombus) species. PLoS ONE 14(6): e0218614.

Gibson KJ, Streich MK, Topping TS, Stunz GW (2019) Utility of citizen science data: A case study in land-based shark fishing. PLoS ONE 14(12): e0226782.

Gouraguine A, Moranta J, Ruiz-Frau A, Hinz H, Reñones O, Ferse SCA, et al. (2019) Citizen science in data and resource-limited areas: A tool to detect long-term ecosystem changes. PLoS ONE 14(1): e0210007.

Hallmann CA, Sorg M, Jongejans E, Siepel H, Hofland N, Schwan H, et al. (2017) More than 75 percent decline over 27 years in total flying insect biomass in protected areas. PLoS ONE 12(10): e0185809.

Larson RN, Brown JL, Karels T, Riley SPD (2020) Effects of urbanization on resource use and individual specialization in coyotes (Canis latrans) in southern California. PLoS ONE 15(2): e0228881.

Lyons E, Zhang L (2019) Trade-offs in motivating volunteer effort: Experimental evidence on voluntary contributions to science. PLoS ONE 14(11): e0224946.

Ožana S, Burda M, Hykel M, Malina M, Prášek M, Bárta D, et al. (2019) Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science. PLoS ONE 14(1): e0210370.

Pescott OL, Walker KJ, Harris F, New H, Cheffings CM, Newton N, et al. (2019) The design, launch and assessment of a new volunteer-based plant monitoring scheme for the United Kingdom. PLoS ONE 14(4): e0215891.

Rasmussen SL, Nielsen JL, Jones OR, Berg TB, Pertoldi C (2020) Genetic structure of the European hedgehog (Erinaceus europaeus) in Denmark. PLoS ONE 15(1): e0227205.

Siljamo P, Ashbrook K, Comont RF, Skjøth CA (2020) Do atmospheric events explain the arrival of an invasive ladybird (Harmonia axyridis) in the UK? PLoS ONE 15(1): e0219335.

Torre M, Nakayama S, Tolbert TJ, Porfiri M (2019) Producing knowledge by admitting ignorance: Enhancing data quality through an “I don’t know” option in citizen science. PLoS ONE 14(2): e0211907.

Wepprich T, Adrion JR, Ries L, Wiedmann J, Haddad NM (2019) Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA. PLoS ONE 14(7): e0216270.


All images used under Pixabay licence.

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