Category Archives: Collections

Introducing the Plant Phenomics & Precision Agriculture Collection

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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 https://doi.org/10.1371/journal.pone.0246872

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 https://doi.org/10.1371/journal.pone.0243923

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 https://doi.org/10.1371/journal.pone.0241528

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 https://doi.org/10.1371/journal.pone.0239591

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 https://doi.org/10.1371/journal.pone.0239673

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 https://doi.org/10.1371/journal.pone.0234703

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 https://doi.org/10.1371/journal.pone.0238530

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 https://doi.org/10.1371/journal.pone.0247243

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!

References

  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. https://doi.org/10.1371/journal.pone.0232595
  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. https://doi.org/10.1371/journal.pone.0246872
  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. https://doi.org/10.1371/journal.pone.0243923
  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. https://doi.org/10.1371/journal.pone.0241528
  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. https://doi.org/10.1371/journal.pone.0239673
  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. https://doi.org/10.1371/journal.pone.0239591
  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. https://doi.org/10.1371/journal.pone.0238173
  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. https://doi.org/10.1371/journal.pone.0242821
  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. https://doi.org/10.1371/journal.pone.0234703
  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. https://doi.org/10.1371/journal.pone.0238530
  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. https://doi.org/10.1371/journal.pone.0247243
  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. https://doi.org/10.1371/journal.pone.0228515

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Introducing the Open Soft Robotics Research Collection

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PLOS ONE is delighted to announce a Collection entitled Open Soft Robotics Research. This Collection consists of research articles submitted to a 2019-2020 Call for Papers on the same topic. As the Collection launches today, it consists of six research articles, while two reviews will be added at a later stage.

Largely inspired by the way many living organisms move and adapt their shape to their surroundings, soft robots have been designed and constructed with compliant, deformable and variable-stiffness materials, sensors and actuators. Biomimicry has allowed soft robots to acquire novel features such as stretchability, growth, morphing, self-reconfigurability, self-healing and edibility. Their impact has grown in a variety of sectors, from search and rescue and exploration, to rehabilitation medicine, surgery, prostheses and exoskeletons, as well as various applications that improve wellness and quality of life.

The papers published today present several exciting aspects of the latest research on the topic of soft robotics. Two papers touch on 3D printing, one for printing surgical devices [1], and one for cores [2] which can be used in a variety of applications. A second set of papers intersect with medicine, in that they provide methods for fabricating prosthetic hands [3] and artificial muscles [4], respectively. Lastly, two of the papers utilise dynamic modelling, one for dielectric elastomer actuators [5] and one for soft continuum manipulators [6]. Taken together, these papers present a fascinating snapshot of the state-of-the-art within soft robotics research.

This Collection was curated by a dedicated team of Guest Editors: Guoying Gu (Shanghai Jiao Tong University), Aslan Miriyev (EMPA, Swiss Federal Laboratories for Materials Science and Technology), Lucia Beccai, (IIT, Istituto Italiano di Tecnologia), Matteo Cianchetti (Scuola Superiore Sant’Anna, School of Advanced Studies Pisa), Barbara Mazzolai (IIT, Istituto Italiano di Tecnologia) and Dana D. Damian (University of Sheffield).

We invite you to explore the Collection starting today, and encourage you to check back in for more Open Soft Robotics Research in PLOS ONE.

References:

[1] Culmone C, Henselmans PWJ, van Starkenburg RIB, Breedveld P (2020) Exploring non-assembly 3D printing for novel compliant surgical devices. PLoS ONE 15(5): e0232952. https://doi.org/10.1371/journal.pone.0232952 

[2] Preechayasomboon P, Rombokas E (2020) Negshell casting: 3D-printed structured and sacrificial cores for soft robot fabrication. PLoS ONE 15(6): e0234354. https://doi.org/10.1371/journal.pone.0234354 

[3] Mohammadi A, Lavranos J, Zhou H, Mutlu R, Alici G, Tan Y, et al. (2020) A practical 3D-printed soft robotic prosthetic hand with multi-articulating capabilities. PLoS ONE 15(5): e0232766. https://doi.org/10.1371/journal.pone.0232766 

[4] Harjo M, Järvekülg M, Tamm T, Otero TF, Kiefer R (2020) Concept of an artificial muscle design on polypyrrole nanofiber scaffolds. PLoS ONE 15(5): e0232851. https://doi.org/10.1371/journal.pone.0232851 

[5] Huang P, Ye W, Wang Y (2020) Dynamic modeling of dielectric elastomer actuator with conical shape. PLoS ONE 15(8): e0235229. https://doi.org/10.1371/journal.pone.0235229 

[6] Tariverdi A, Venkiteswaran VK, Martinsen ØG, Elle OJ, Tørresen J, Misra S (2020) Dynamic modeling of soft continuum manipulators using lie group variational integration. PLoS ONE 15(7): e0236121. https://doi.org/10.1371/journal.pone.0236121 

Featured Image credit: UC San Diego Jacobs School of Engineering CC-BY 2.0

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Introducing PLOS ONE’s Education Research Collection

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Understanding teaching and learning—what works, how, and for whom—is an academic endeavor in its own right. This may be conducted by medical researchers who are also educators or by education scholars whose main expertise is in pedagogy or educational psychology. As PLOS ONE welcomes rigorous original research regardless of disciplinary boundaries, it is a home for education research. Our journal welcomes a variety of study designs and methods, including quantitative research, but importantly also for education research, mixed-methods and qualitative research.

The newly published Education Research Collection illustrates the breadth of contributions made in PLOS ONE to this field over the years. The Collection includes both small-scale interventions (such as on the teaching of fractions related to Common Core State standards [1]) and curriculum-wide observations (for example, of the most effective forms of active learning in biology classrooms [2]). It ranges from early childhood development (such as the assessment of the Early Childhood Environment scale [3]) to higher education faculty professional development programs (for instance, on changing teaching practices of science faculty [4]).


Credit: Kimberly Farmer

The Collection includes a variety of study types, whether randomized control trials (such as the assessment of educational tools [5]),  large longitudinal studies (such as on the long-term effects of the early childhood Chicago School Readiness Project [6]), or systematic reviews and meta-analyses (such as on the effect of child-staff ratios in early childhood education [7]). It highlights innovative programs (for instance on teaching critical thinking skills and argumentation through bioethics education [8]) and novel teacher assessment tools (for instance in medical education [9]).

This Collection also includes studies on the gender gap in STEM education, such as the effect of an intervention on gender ratios in higher education [10] or the analysis of multinational PISA data [11].

The papers in this Collection also include several studies on teacher attitudes that can be relevant to their professional development, whether on teachers’ attitude toward the inclusion of students with disabilities [12], on teachers’ emotions [13], or the role of teachers’ expectations about children’s socio-economic status and their performance [14].

This is only a small selection of the education research published at PLOS ONE over the years, and we welcome new submissions to this Collection.

For authors who are new to education research

If you want to know more about methodological and reporting standards in the field, we can recommend some useful resources such as:

  • American Psychologist’s Journal Article Reporting standards for both quantitative research (Appelbaum et al. 2018 [15]) and qualitative research (Levitt et al. 2018 [16]).
  • Annotated education research articles at the CBE-Life Science Education journal’s website (published by the American Society of Cell Biology).
  • The Institute of Education Sciences’ resources for researchers.

For papers describing new methods or programs, including teaching methods and class interventions, PLOS ONE has specific criteria of utility, validation, and availability (see more here). 


Credit: Jess Bailey

In general, we expect sufficient methodological details enabling other teachers and researchers to replicate a teaching intervention such as sample worksheets, a detailed lesson plan or curriculum or other educational materials. For any intervention, we look for sufficient details to assess its generalizability: how students were recruited, the frequency of class meetings, teachers’ experience, teaching objectives, school setting, but also detailed assessment methods and a comparison with existing methods. Educational evidence may consist both in quantitative assessments (such as pre/post test results) and qualitative evidence (such as student works and testimonies). 

We also expect papers to provide sufficient background about the study they report to embed its rationale in relevant scholarly discussions about education theory or motivate a pedagogical intervention with reference to teaching standards, when applicable.

We look forward to your continuing submissions in education research to PLOS ONE and are excited to see this Collection grow in the years to come!   

References

[1] Fazio, L. K., Kennedy, C. A., & Siegler, R. S. (2016). Improving children’s knowledge of fraction magnitudes. PLOS ONE, 11(10), e0165243.

[2] Weir, L. K., Barker, M. K., McDonnell, L. M., Schimpf, N. G., Rodela, T. M., & Schulte, P. M. (2019). Small changes, big gains: A curriculum-wide study of teaching practices and student learning in undergraduate biology. PLOS ONE, 14(8), e0220900.

[3] Brunsek, A., Perlman, M., Falenchuk, O., McMullen, E., Fletcher, B., & Shah, P. S. (2017). The relationship between the Early Childhood Environment Rating Scale and its revised form and child outcomes: A systematic review and meta-analysis. PLOS ONE, 12(6), e0178512.

[4] Bush, S. D., Rudd, J. A., Stevens, M. T., Tanner, K. D., & Williams, K. S. (2016). Fostering change from within: Influencing teaching practices of departmental colleagues by science faculty with education specialties. PLOS ONE, 11(3), e0150914.

[5] Diamond, A., Lee, C., Senften, P., Lam, A., & Abbott, D. (2019). Randomized control trial of Tools of the Mind: Marked benefits to kindergarten children and their teachers. PLOS ONE, 14(9), e0222447.

[6] Brunsek, A., Perlman, M., Falenchuk, O., McMullen, E., Fletcher, B., & Shah, P. S. (2017). The relationship between the Early Childhood Environment Rating Scale and its revised form and child outcomes: A systematic review and meta-analysis. PLOS ONE, 12(6), e0178512.

[7] Perlman, M., Fletcher, B., Falenchuk, O., Brunsek, A., McMullen, E., & Shah, P. S. (2017). Child-staff ratios in early childhood education and care settings and child outcomes: A systematic review and meta-analysis. PLOS ONE, 12(1), e0170256.

[8] Chowning, J. T., Griswold, J. C., Kovarik, D. N., & Collins, L. J. (2012). Fostering critical thinking, reasoning, and argumentation skills through bioethics education. PLOS ONE, 7(5), e36791.

[9] Arah, O. A., Hoekstra, J. B., Bos, A. P., & Lombarts, K. M. (2011). New tools for systematic evaluation of teaching qualities of medical faculty: results of an ongoing multi-center survey. PLOS ONE, 6(10), e25983.

[10] Sullivan, L. L., Ballen, C. J., & Cotner, S. (2018). Small group gender ratios impact biology class performance and peer evaluations. PLOS ONE, 13(4), e0195129.

[11] Stoet, Gijsbert, and David C. Geary. “Sex differences in mathematics and reading achievement are inversely related: Within-and across-nation assessment of 10 years of PISA data.” PLOS ONE 8.3 (2013): e57988.

[12] Vaz, S., Wilson, N., Falkmer, M., Sim, A., Scott, M., Cordier, R., & Falkmer, T. (2015). Factors associated with primary school teachers’ attitudes towards the inclusion of students with disabilities. PLOS ONE, 10(8), e0137002.

[13] Frenzel, A. C., Becker-Kurz, B., Pekrun, R., & Goetz, T. (2015). Teaching this class drives me nuts!-Examining the person and context specificity of teacher emotions. PLOS ONE, 10(6), e0129630.

[14] Speybroeck, S., Kuppens, S., Van Damme, J., Van Petegem, P., Lamote, C., Boonen, T., & de Bilde, J. (2012). The role of teachers’ expectations in the association between children’s SES and performance in kindergarten: A moderated mediation analysis. PLOS ONE, 7(4), e34502.

[15] Appelbaum, M., Cooper, H., Kline, R. B., Mayo-Wilson, E., Nezu, A. M., & Rao, S. M. (2018). Journal article reporting standards for quantitative research in psychology: The APA Publications and Communications Board task force report. American Psychologist, 73(1), 3.

[16] Levitt, H. M., Bamberg, M., Creswell, J. W., Frost, D. M., Josselson, R., & Suárez-Orozco, C. (2018). Journal article reporting standards for qualitative primary, qualitative meta-analytic, and mixed methods research in psychology: The APA Publications and Communications Board task force report. American Psychologist, 73(1), 26.

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Introducing the Microbial Ecology of Changing Environments Collection

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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.

References

  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. https://doi.org/10.1371/journal.pone.0238405
  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. https://doi.org/10.1371/journal.pone.0235441
  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. https://doi.org/10.1371/journal.pone.0235225
  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. https://doi.org/10.1371/journal.pone.0231187
  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. https://doi.org/10.1371/journal.pone.0237335
  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. https://doi.org/10.1371/journal.pone.0237869

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

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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!

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Introducing the Biodiversity Conservation Collection

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  It is with great pleasure that we announce the launch of our Biodiversity Conservation Collection. This Collection showcases research on a broad range of conservation science related topics, including anthropogenic impacts on biodiversity, such

Introducing the Biodiversity Conservation Collection

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It is with great pleasure that we announce the launch of our Biodiversity Conservation Collection. This Collection showcases research on a broad range of conservation science related topics, including anthropogenic impacts on biodiversity, such as habitat degradation, the spread of invasive species and global warming; conservation of key ecosystem services, such as carbon sequestration and pest regulation; and new management strategies to prevent further biodiversity loss.

We are extremely grateful to our team of Guest Editors, Steve Beissinger (University of California, Berkeley), Thomas Couvreur (Pontificia Universidad Catolica del Ecuador), Carlos Duarte (KAUST), Claudia Mettke-Hoffmann (Liverpool John Moores University) and Stuart Pimm (Duke University), for evaluating all submitted research and selecting articles for inclusion in the Collection. We also want to express our thanks to the PLOS ONE Academic Editors involved in the handling of submissions, to the reviewers, and to all the authors who submitted their research to this Call for Papers.

 

 

Habitat loss

Eight of the studies published in the initial Collection release focus on habitat destruction in a wide range of regions, ecosystems and species. In the North Pacific Ocean, Edwards et al. investigated the ecological consequences of marine deforestation caused by shifting trophic interactions in the Aleutian Archipelago. They show that the rapid decline of sea otter populations, caused by increased predation pressure from killer whales, led to high sea urchin densities causing widespread deforestation of the kelp forests and general loss of biodiversity and ecosystem function. In the mainland USA, Bradshaw et al. evaluated whether wetland management practices for waterfowl were also beneficial to other wetland-dependent species such as bitterns, grebes and crakes. Habitats for marsh bird species have more than halved in the last 50 years due to wetland loss and degradation; their results highlight the importance of maintaining wetland hydrologic and vegetation complexity for the conservation of breeding marsh birds.

In Brazil, three independent studies provide evidence of the impacts of habitat fragmentation in the Amazon rain forest, where biodiversity has rapidly declined in recent decades. Palmeirim et al. quantified the effect of deforestation on small mammals and found that forest dwelling species are being replaced by open-habitat species as the deforestation frontier expands. Teixeira-Santos et al. studied four endangered emblematic large terrestrial mammals and showed that the survival ability was different for each species and that some species can adapt to tolerate anthropogenically altered habitats. Paschoalini et al. studied the effects of habitat fragmentation on the Araguaian river dolphin, whose populations have been dramatically reduced due to dam construction. This research provides potential practical applications to help species management and conservation in the region, as occupation and development of the Amazon is currently being encouraged in Brazil.

 

 

When the habitat is fragmented, isolated populations lose genetic diversity, leaving them more vulnerable to changing environmental conditions and with a higher risk of extinction. In the Midwestern USA, Douglas et al. examined the genetic population structure of three upland game birds inhabiting the declining American prairie grasslands, including the endangered Greater Prairie Chicken, and found that their populations are experiencing a genetic bottleneck. They advocate for a multi-species approach as a more effective management strategy for endangered upland game birds and for making more land available to prairie species. In the United Kingdom, Ball et al. conducted a study on the conservation genetic state of adder populations and found that the species’ polyandrous breeding system is, for the moment, protecting it against inbreeding. However, this might become a problem in the future as loss of connectivity prevents movement of individuals between patches of suitable habitat. Dondina et al. studied the suitability of ecological corridors to connect two isolated wolf populations through the degraded lowlands of Northern Italy and showed the importance of keeping natural areas, such as rivers, for maintaining habitat connectivity for the conservation of endangered species in a fragmented landscape.

 

 

Climate change

Three studies among the first batch of articles published in this Collection address the impacts of climate change on biodiversity and potential mitigation strategies. Carbon sequestration has been suggested as a potential approach to mitigating the effects of greenhouse gas emissions responsible for global warming. In Spain, Morant et al. investigated the relationships between wetlands’ ecological characteristics, conservation measures and carbon emissions in the Ebro Delta wetlands. Wetlands are an important ecosystem service acting as natural carbon sinks but are under threat due to habitat destruction. 

Large-scale empirical studies of the existing and projected impacts of climate change on wildlife are vital to scientifically-informed conservation management strategies aimed at minimizing and mitigating these impacts. In Southern California, Fogarty et al. used a large bird abundance dataset to investigate whether annual variation in seasonal temperature and precipitation was associated with relative abundances of breeding bird species. They found that species in arid areas may be negatively affected by increased temperature and aridity, but species from cooler areas may respond positively to those fluctuations in climate. Carbon pricing policies can also have unintended consequences for biodiversity through changing land management. Hashida et al. modelled forest habitat changes in response to forest landowner decision-making under multiple carbon pricing scenarios in Western USA. Their results predict a major shift from coniferous forest to hardwoods which could result in a dramatic loss of biodiversity in the region.

 

 

Invasive species

Three studies published in the Collection showcase research on species invasions. International trade is a major pathway of introduction of invasive species. Lucardi et al. conducted a comprehensive survey of the plant community at the largest container terminal in the USA . Their research identified the presence of a high number of invasive plant species in the port, providing  important evidence that shipping ports are crucial sources of emergent plant invasions but  are largely under-researched. Invasive species can have complex ecological impacts on the regions of invasion. Besterman et al. studied the ecological impacts of the establishment of one of the most invasive macroalgae on habitat selection and foraging behaviour of shorebirds in the mid-Atlantic region of the USA and found that generalist species preferred invaded habitats while specialist shorebirds preferred uninvaded mudflats. Invasive species also cause major economic losses in the regions of invasion. One of the most successful methods for sustainable management of invasive species is using their own natural enemies against them. In Morocco, Qessaoui et al. discovered the insecticidal activity of native rhizobacteria present in the soil against an important pest of tomato crops and suggested that using biological control agents would reduce the amount of synthetic chemical pesticides being used to control plant pests.

 

 

Conservation strategies

Finally three papers report methodological advances in conservation of endangered species. Endangered species are usually difficult to study because their population densities are low which hampers conservation efforts. Here, Nagarajan et al. report successful results of a non-invasive method for monitoring a wood-boring beetle species threatened by habitat loss in California. Current monitoring efforts require extensive field work looking for this rare species. In this study, the authors collected faecal samples from exit holes on trees and applied genetic barcoding techniques to identify the makers of the holes.

Large terrestrial carnivores are often keystone species in the ecosystems but have historically been persecuted and their populations are in decline globally. In the USA, sport hunting is used as a tool for managing puma populations. Laundré et al. investigated the effectiveness of this strategy for reducing conflict with humans, livestock and game species. Their results indicate that there is little evidence that puma control reduces conflict, and remark the need to reassess traditional predator control practices.

Management of captive populations is crucial for conservation of endangered species whose wild populations are at high risk of extinction. Fazio et al. studied the stress physiology of the fishing cat, a threatened wild cat from Southeast Asia, that is notoriously difficult to breed in captivity. Their study suggests that management actions such as transfers between facilities increases levels of stress while reduced animal-keeper interaction and social housing could lower stress levels and increase breeding success. This study might provide insights to better manage translocations of captive individuals of easily stressed species.

 

 

At the time of launch, there are 17 research articles featured in the Collection but more papers will be added as they are published over the coming weeks – so do check back for updates!

 

About the Guest Editors:

Steve Beissinger

Steve Beissinger is Professor of Ecology & Conservation Biology at the University of California, Berkeley, where he held the A. Starker Leopold Chair in Wildlife Biology (2003-13), is a research associate of the Museum of Vertebrate Zoology, and is the co-Director of the Berkeley Institute for Parks, People and Biodiversity. Professor Beissinger’s current research centers on wildlife responses to global change and species’ extinctions – with recent fieldwork carried out in protected areas and working landscapes in California and Latin America. He directs the Grinnell Resurvey Project – a 15 year effort to revisit locations throughout California first surveyed by Joseph Grinnell in the early 1900’s in order to quantify the impacts of a century of climate and land-use change on the birds and mammals of California. Steve’s studies of parrotlets in Venezuela extend more than 30 years. Integrative studies of secretive, threatened rails in California provide a model for understanding coupled natural and human systems. He has authored over 200 scientific publications and is senior editor of three books. He served on the editorial boards of Ecology Letters, Ecology, Conservation Biology, Studies in Avian Biology, and Climate Change Responses. Steve is a Fellow of the American Association for the Advancement of Science, the Ecological Society of America (ESA), the Wissenschaftskolleg zu Berlin, and the American Ornithological Society, which awarded him the William Brewster Memorial Award in 2010 for his research on Western Hemisphere birds.

Thomas Couvreur

Thomas L.P. Couvreur is a senior researcher at the French National Institute for Sustainable Development, and is currently based at the “Pontificia Universidad Catolica del Ecuador”, in Quito Ecuador. He received his PhD in tropical biodiversity from the Wageningen University in the Netherlands, and worked as post doc at the Osnabruck University in Germany and The New York Botanical Garden in the USA. His main interest lies in understanding the evolution, resilience and diversity of tropical biodiversity, and rain forests in particular, one of the most complex and diverse ecosystems on the planet. He undertakes research in taxonomy, conservation, molecular phylogenetics and phylogeography of tropical plants. His research mainly focuses on tropical Africa and South America. He is chair of the IUCN Species Survival Commission for palms since 2018.

 Carlos Duarte

Professor Carlos M. Duarte (Ph.D. McGill University, 1987) is the Tarek Ahmed Juffali Research Chair in Red Sea Ecology at the King Abdullah University of Science and Technology (KAUST), in Saudi Arabia. Before this he was Research Professor with the Spanish National Research Council (CSIC) and Director of the Oceans Institute at The University of Western Australia.
Duarte’s research focuses on understanding the effects of global change in aquatic ecosystems, both marine and freshwater. He has conducted research across all continents and oceans, spanning most of the marine ecosystem types, from inland to near-shore and the deep sea and from microbes to whales. Professor Duarte led the Malaspina 2010 Expedition that sailed the world’s oceans to examine the impacts of global change on ocean ecosystems and explore their biodiversity. Professor Duarte served as President of the American Society of Limnology and Oceanography between 2007 and 2010. In 2009, was appointed member of the Scientific Council of the European Research Council (ERC), the highest-level scientific committee at the European Level, where he served until 2013. He has published more than 700 scientific papers and has been ranked within the top 1% Highly-Cited Scientist by Thompson Reuters in all three assessments of this rank, including the 2018 assessment released by Clarivate Analytics.

 Claudia Mettke-Hofmann

Dr Claudia Mettke-Hofmann is Reader in Animal Behaviour at Liverpool John Moores University, UK, and Subject Leader of the Animal Behaviour team. She received her externally conducted PhD from Free University of Berlin, Germany, and subsequently worked as a postdoc at the Max-Planck Institute for Ornithology in Radolfzell and Andechs, Germany, in collaboration with the Konrad Lorenz Institute for Comparative Behaviour, Vienna, Austria, before moving to the Smithsonian Migratory Bird Center, Washington DC, USA. She is now based at Liverpool John Moores University. Her research area is cognitive ecology, mainly in birds, with strong links to conservation aspects and animal welfare. She investigates how animals collect and store environmental information in relation to their ecology on the species level but also on the individual level (personality). A focus is how animals respond to environmental change, particularly in species that differ in their movement patterns such as being resident, migratory or nomadic. Differences in cognitive abilities in these groups help explain and predict population developments in our rapidly changing environments. More recently, her research has focussed on individual differences in cognition in colour-polymorphic species highlighting exciting differences in responses to environmental change between colour morphs. Claudia has been a PLOS ONE Section Editor since 2014.

 Stuart Pimm

Stuart Pimm is the Doris Duke Chair of Conservation Ecology at the Nicholas School of the Environment at Duke University. He is a world leader in the study of present day extinctions and what we can do to prevent them. Pimm received his BSc degree from Oxford University in 1971 and his Ph.D from New Mexico State University in 1974. Pimm is the author of over 300 scientific papers and four books. Pimm directs SavingSpecies, a 501c3 non-profit that uses funds for carbon emissions offsets to fund local conservation groups to restore degraded lands in areas of exceptional tropical biodiversity. His international honours include the Tyler Prize for Environmental Achievement (2010), the Dr. A.H. Heineken Prize for Environmental Sciences from the Royal Netherlands Academy of Arts and Sciences (2006).

 

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Stem Cell Plasticity in Tissue Repair and Regeneration Collection

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We are excited to publish a collection entitled Stem Cell Plasticity in Tissue Repair and Regeneration, which results from a PLOS ONE’s call for papers announced last year. We encouraged submissions spanning a broad range of biomedical topics, including basic stem cell biology, preclinical research and biomedical engineering. The papers included in the collection provide examples of how the dynamic functions of stem cells can be harnessed to regenerate damaged or lost tissues. Regenerative approaches may offer a unique therapeutic opportunity for diseases where with no established treatments exist.

 

In line with PLOS ONE publication ethos, we welcomed solid and clearly reported studies regardless of the perceived impact and positive nature of the main findings. We think that in the fast-paced field of stem cell research, addressing publication bias is particularly important to advance knowledge and bring new therapies to the clinic.

 

Two studies included in the collection reported the role and regenerative ability of adult mesenchymal stem cells (MSCs). Chung et al. showed the regenerative potential of human MSCs in a rat model of bladder disease. They also identified the bladder submucosa as the most effective route of MSC administration. In a clinical study among patients with acute respiratory distress syndrome, Patry et al. found that extracorporeal membrane oxygenation increased the number of circulating MSCs, although further research is needed to establish the regenerative potential of these cells in the context of pulmonary disease.

 


Bladder tissue regeneration identified via IHC staining pone.0226390

 

Two methodological papers focused on the differentiation of human induced pluripotent stem cells (hiPSCs) into cardiac cells. This rapidly evolving research area aims at overcoming the current challenges in generating mature cells in large quantity and high purity for tissue engineering applications. Rupert et al. described practical methods for the optimization of hiPSC-cardiomyocyte differentiation, highlighting the key role of metabolic selection. Chu et al. demonstrated that cardiac differentiation can be achieved by co-culturing hiPSCs with mature cardiomyocytes, without the addition of exogenous pharmacological agents.

 


Workflows for cardiac differentiation of stem cells pone.0230001

 

This collection was made possible thanks to the fantastic work of our Guest Editors – Michelina Iacovino, Scott D. Olson and Che Connon – who helped develop the scope of the call for papers and evaluated all submitted research for inclusion in the collection. We are also extremely grateful to the members of our editorial board and external peer-reviewers for dedicating their time and expertise to the evaluation of submissions.

 

We will add new papers to the Collection as they are published, so we invite you to check back the collection webpage in the coming weeks. If you are interested in keeping up to date with the latest stem cell research from the broader literature, check out our PLOS Channel too.

 

Guest Editors

Scott D. Olson

Scott Olson is a mesenchymal stem cell (MSC) Biologist working in the Children’s Program in Regenerative Medicine in the Department of Pediatric Surgery at McGovern School of Medicine. Dr. Olson completed his doctorate in the lab of Dr. Darwin Prockop at Tulane University’s Center for Gene Therapy studying novel methods by which MSCs can contribute to tissue repair. At University of California at Davis’s Health Sciences Institute for Regenerative Cures with Dr. Jan Nolta, Dr. Olson worked to apply MSCs as a platform to develop new treatments for Huntington’s Disease. Dr. Olson joined UTHealth in September 2011.

 

Dr. Olson is involved in developing and transitioning studies with direct translational applications. At UT Health, his primary focus is bringing his expertise in the field of adult stem cells, specifically MSCs, to explore their potential in the treatment of Traumatic Brain Injury (TBI) and in trauma-associated neuroinflammation in general. MSCs have been used in a number of completed, ongoing, and proposed clinical trials with reported therapeutic benefits. Dr. Olson strives to better describe the role of MSCs in injuries of the central nervous system, highlighting their innate therapeutic abilities in an effort to create an improved treatment for TBI.

 

Michelina Iacovino

Michelina Iacovino is an Assistant Professor at the David Geffen School of Medicine at The University of California, Los Angeles (UCLA), and a Principal Investigator at Los Angeles Biomedical Research Institute (LABioMed) at Harbor-UCLA in the Pediatrics Department.

She obtained her Doctorate in Italy in Biochemistry and Applied Chemistry working on mitochondrial DNA inheritance in yeast in collaboration with Dr. Ronal Butow at the University of Texas Southwestern Medical Center. She then trained in the field of hematopoietic stem cells with Dr. Michael Kyba during her postdoctoral fellowship, studying the role of Hox genes during blood development. She joined LABioMed in 2012, extending her expertise of stem cell biology to develop treatments for rare lysosomal disorders that affect brain function. She is currently developing a stem cell therapy for Sanfilippo syndrome, an incurable and rare lysosomal disorder, using neural progenitor cells.

 

Che Connon

Che Connon obtained his PhD in Biophysics from the Open University Oxford Research Unit in 2000, during which time (under the supervision of Professor Keith Meek) he investigated corneal wound healing and transparency. He subsequently obtained a JSPS post-doctoral fellowship to work with Professor Shigeru Kinoshita in Kyoto, Japan for two years studying corneal stem cell transplantation. Upon his return to the UK he was awarded a Royal Society Fellowship to investigate the use of biomaterials in stem cell therapies. He obtained his first permanent position in 2007 at University of Reading, School of Pharmacy and since 2014 he has held the position of Professor of Tissue Engineering at Newcastle University.

Professor Connon’s research team seeks to engineer functional replacement and temporary ‘bridge’ tissues using a modular approach while also developing model systems to study physiological and pathophysiological corneal tissue formation. He is currently working with smart (cell responsive) biomaterials, characterizing the mechanical and geometric environment of the corneal stem cell niche and 3D printing the corneal stroma.

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