RIO Journal’s Post

I'm officially a published author in the Journal of Experimental Marine Biology and Ecology! 📚 🔬 🌊 This would not be possible without my mentor, Florian. Your belief in me and your dedication to nurturing my passion for marine ecology has been invaluable. Thank you for always showing patience and compassion as I navigated this thesis project, along with your encouragement to ask difficult questions, take risks, and not be afraid to make mistakes. This achievement would not have been possible without you! Feel free to check out our paper below. Here's to many more discoveries ahead! #Research #MarineEcology

We've talked about flora, fauna and funga in isolation, today let's talk about an intersection of these worlds - the rhizosphere. For those not up to speed on their soil science, which if we're honest is a lot of us, the rhizosphere is the zone of soil surrounding the plant root. It's only about 1mm wide, but there's a lot going on and the zone plays a crucial role in diverse ecosystem functions including water and carbon fluxes as well as soil microbiology. A recently published article in Soil Science puts forward dynamic modeling of the rhizosphere looking at pore spaces. The findings demonstrate the interactions between plant and soil can lead to structural and textural changes in the soil in the vicinity of the root, demonstrated to persist for upwards of 1000 days. At a basic level, root / soil interactions lead to a fundamental change in the porosity (void fractions) of the rhizosphere. Long gone are the days where we held a concept of a one-way route from soil to plant for nutrients. Interestingly this particular research is a contribution from mathematicians and machine learning experts. The multi-disciplinary team needed to deepen our understanding of soil microbiology is reflective of the complexity and dynamism of this fascinating 1mm-wide space. #sustainableagriculture #soilscience https://lnkd.in/gQKgDbsz

How small a PCR volume can you use for PCR and metabarcoding to save reagents and money, and does it have any effect on the results? Here’s an encouraging article from Buchner et al. (2021) that found no significant differences in metabarcoding results using PCRs of 5 µl to 50 µl volumes, and supporting the use of low volumes (subject to liquid handling constraints and lack of PCR inhibitors in the samples): Buchner et al. (2021). Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecology and evolution, 11(13), 9092-9099. https://lnkd.in/ebf7JaTY

A new paper, co-authored by Connecticut Academy of Science and Engineering Member Gene Likens, Distinguished Research Professor in the University of Connecticut Department of Ecology and Evolutionary Biology, reveals that human activities are disrupting the natural salt cycle - making Earth’s air, soil, and freshwater saltier. Mining, land development, agriculture, construction, water and road treatment, and other industrial activities can intensify salinization, which harms biodiversity and makes drinking water unsafe. https://buff.ly/3QL1crL #climate #ecology #environment #salinization #biodiversity

🔍 Data Discovery | Great Western Woodlands BASE Contextual, Soil Physico-Chemical Data Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. Soil collection and analysis of chemical and physical attributes was carried out at the Great Western Woodlands site to provide contextual data for the Biomes of Australian Soil Environments (BASE) soil microbial diversity project. BASE has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. Access the data on the TERN Data Discovery Portal ⤵ 🔗 https://lnkd.in/gievC-bx #datadiscovery #data #research #soil #ecosystem #ecology (Image: Position of BASE sample sites, August 2015)

🌿🔬 Introducing a new YouTube channel that's turning over a new leaf in the world of soil biology! 🌍 🎬 Check out Agrogate's debut video, where they explore the hidden universe beneath our feet. Discover how soil organisms, from bacteria and fungi to insects and plant roots, are the unsung heroes of our ecosystem. 🌱 Learn about their crucial roles in nutrient cycling, water dynamics, and disease suppression. Dive into the fascinating world of the rhizosphere and the symbiotic relationships that shape plant health and productivity. 👩🔬 Led by two passionate soil biologists, Agrogate is your go-to channel for understanding the intricate web of life that makes our planet thrive. Whether you're a gardening enthusiast, an environmentalist, or simply curious about the natural world, this channel is a goldmine of knowledge. 📽️ Don't miss out on this enlightening journey. Watch the first video and subscribe to Agrogate to stay updated on the latest discoveries in soil biology. #SoilBiology #AgrogateChannel #EcosystemBalance #SustainableAgriculture #Rhizosphere #MicrobialWonders #NaturalWorld #Education #EnvironmentalScience #SubscribeNow

We all need to reduce our impact in the age of climate change, but fish seem to be taking this to heart: many species are “shrinking” as waters grow warmer.    It’s not for the reasons we thought, however: a collaborative team of scientists led by Joshua Lonthair and Lisa Komoroske of the College of Natural Sciences at UMass Amherst’s departments of Biology and Environmental Conservation, respectively, recently found that there is no physiological evidence supporting a leading theory for this shrinking of fish size, which involves the surface area of fish gills.    The results of the study were recently published in the "Journal of Experimental Biology."    Learn more: https://lnkd.in/e2r9vuXT    #CNS #UMassBiology #UMassEco #Biology #ClimateChange #Oceans #Fish 

We have just published a new paper that sheds light on one of Darwin's "abominable mysteries" - the remarkable diversity of flowering plants, with a great international team of authors, lead by Dimitar Dimitrov, Zhiheng Wang and myself. The paper is entitled: Diversification of flowering plants in space and time and published in Nature Communications. https://rdcu.be/dr55I It contains a new global phylogeny of all flowering plants (14,244 genera) and their global distributions, with associated analyses of diversity patterns in time and space. In total, the raw data for our phylogenetic analyses included 669,619 records of seed plant DNA sequences for 132,373 infrageneric taxa and 457 families. And the global distribution data set includes millions of province-level distribution records from > 1100 available data sources Key Findings: 🌸 Early Cretaceous Surge: Flowering plants experienced a significant increase in diversification rates during the early Cretaceous. 🦕 Stability Post-Cretaceous: A period of stable or slightly decreased diversification rates followed until the end of the Cretaceous–Paleogene mass extinction event, 66 million years ago. 🌳 Modern Resurgence: A notable uptick in diversification rates is observed from the post-mass extinction era to the present day. Our analysis highlights intriguing geographical and temporal patterns: 🏜️ Temperate and Dryland Flora: Younger genera with high diversification rates are prevalent in these regions. 🌴 Tropical Diversity: Older genera with lower diversification rates are dominant, presenting a negative correlation with spatial diversification patterns. 🌍 This comprehensive study not only enhances our understanding of plant evolution but also underscores the influence of global changes since the Cenozoic era on the distribution and diversity of flowering plants.

Interpreting eDNA detections requires careful consideration. However, by considering multiple lines of evidence and using a quantitative model, we can improve the accuracy of our estimates! A study by Reid Tingley, Rhys Coleman, Nathaniel Gecse, Anthony van Rooyen, and Andrew Weeks offers a great example of how this can be done! 🧩 Occupancy Modeling: The researchers used a hierarchical site occupancy-detection model to estimate the probability of species presence at each site based on eDNA data. The model also considered false positive and false negative errors. 📊 Calibration Experiments: The researchers conducted a calibration experiment to fine-tune their model. They filtered, extracted, and analyzed distilled water samples using the same procedure as the field samples. This experiment helped them estimate the probability of false positive detections and refine the model parameters. 🎣 Leveraging Multiple Data Sources: By incorporating survey data from an unambiguous species detection method, such as dip-netting, along with the eDNA data, the researchers were able to improve their estimation of parameters related to eDNA detection and false positive detections. 🔢 Optimizing Replicates: The model estimates detection probability by considering the number of replicates, which provides insights into sampling efficiency. This helps researchers determine the appropriate number of replicates for reliable species detection, which is valuable information for future eDNA sampling! Reference for the occupancy model the researchers used 👉 Guillera‐Arroita, G., Lahoz‐Monfort, J. J., van Rooyen, A. R., Weeks, A. R., & Tingley, R. (2017). Dealing with false‐positive and false‐negative errors about species occurrence at multiple levels. Methods in Ecology and Evolution, 8(9), 1081-1091. Share your insights, questions, and thoughts in the comments below!  #eDNAconservation. #ConservationScience #EnvironmentalDNA #Biodiversity

Our lab published a new paper using hyperspectral data to identify invasive tree species. The novelty is to use DL for training data augmentation and we thoroughly analysed the appropriate segmentation parameters in post-classification. Results were best with sporadic-like trees (such as Ailanthus), the map with our approach showed tree crowns instead of spatially sparsed pixels. https://lnkd.in/dSvhztEz