Article
Geosciences, Multidisciplinary
Wen Xing, Xiaoming Lu, Shuli Niu, Dima Chen, Jinsong Wang, Ya Liu, Bingxue Wang, Shuang Zhang, Zhaolei Li, Xijun Yao, Qiang Yu, Dashuan Tian
Summary: Nitrogen deposition has a significant impact on soil nematodes, reducing their diversity and altering their abundance depending on climate conditions. High trophic-level nematodes are more vulnerable to nitrogen-induced effects than low-level nematodes. This study highlights the potential consequences of increased nitrogen loads on soil food webs and ecosystem functioning.
Article
Ecology
Leiyi Chen, Yuanhe Yang
Summary: The study points out that overlooking the non-linear relationship between topsoil Delta C-14 and plant carbon input in Wu et al.'s analysis is the key reason for the disagreement between their findings and the findings of this study. Despite this, plant carbon input remains the main factor influencing topsoil carbon turnover.
Article
Microbiology
Muhammad Atif Muneer, Xiaoman Huang, Wei Hou, Yadong Zhang, Yuanyang Cai, Muhammad Zeeshan Munir, Liangquan Wu, Chaoyuan Zheng
Summary: The study investigated the responses of soil fungal communities and functions to different nutrient management practices in red soils. The results showed that these practices significantly increased soil pH and alpha diversity indices of soil fungal communities. FUNGuild analysis revealed that arbuscular mycorrhizal fungi and ectomycorrhizal fungi were more abundant under nutrient management practices, while pathogenic fungi were less abundant.
Editorial Material
Multidisciplinary Sciences
Shonali Pachauri, Setu Pelz, Christoph Bertram, Narasimha D. Rao, Keywan Riahi
Summary: We appreciate Semieniuk et al.’s analysis as a supplementary perspective to highlight the unequal distribution of regional investment capabilities in addressing climate change. Our study is based on the estimates from the Intergovernmental Panel on Climate Change (IPCC) WGIII's sixth assessment report (AR6), which consider regional differences in technology costs and use both purchasing power parity (PPP) and market exchange rates (MERs). We utilize these IPCC estimates to explore the question of how much regional investments should be financed within each region, taking fairness into consideration.
Editorial Material
Multidisciplinary Sciences
Alan Cooper, Chris S. M. Turney, Jonathan Palmer, Alan Hogg, Matt McGlone, Janet Wilmshurst, Andrew M. Lorrey, Timothy J. Heaton, James M. Russell, Ken McCracken, Julien G. Anet, Eugene Rozanov, Marina Friedel, Ivo Suter, Thomas Peter, Raimund Muscheler, Florian Adolphi, Anthony Dosseto, J. Tyler Faith, Pavla Fenwick, Christopher J. Fogwill, Konrad Hughen, Matthew Lipson, Jiabo Liu, Norbert Nowaczyk, Eleanor Rainsley, Christopher Bronk Ramsey, Paolo Sebastianelli, Yassine Souilmi, Janelle Stevenson, Zoe Thomas, Raymond Tobler, Roland Zech
Summary: The study suggests that geomagnetism plays a role in environmental and evolutionary changes, and further testing with new data is needed. The studies presented by Picin et al. do not undermine the model proposed by the researchers.
Editorial Material
Multidisciplinary Sciences
Alan Cooper, Chris S. M. Turney, Jonathan Palmer, Alan Hogg, Matt McGlone, Janet Wilmshurst, Andrew M. Lorrey, Timothy J. Heaton, James M. Russell, Ken McCracken, Julien G. Anet, Eugene Rozanov, Marina Friedel, Ivo Suter, Thomas Peter, Raimund Muscheler, Florian Adolphi, Anthony Dosseto, J. Tyler Faith, Pavla Fenwick, Christopher J. Fogwill, Konrad Hughen, Matthew Lipson, Jiabo Liu, Norbert Nowaczyk, Eleanor Rainsley, Christopher Bronk Ramsey, Paolo Sebastianelli, Yassine Souilmi, Janelle Stevenson, Zoe Thomas, Raymond Tobler, Roland Zech
Summary: The paper on the impacts of the Laschamps Geomagnetic Excursion 42,000 years ago has generated significant interest from both the scientific community and the public, particularly regarding the so-called Adams Event related to the initial transition of the magnetic poles. The authors are open to discussing their new ideas, but are disappointed by Hawks' claims of misrepresentation, especially given his limited review of the material.
Article
Green & Sustainable Science & Technology
Xuli Chen, Manfei Wang, Fujia Wu, Bo Sun, Tianyu Yang, Huixing Song
Summary: This study analyzed the chemical properties and microbial diversity of soils covered by different organisms on the Leshan Giant Buddha body, finding that concentrations of organic carbon, nitrogen, and phosphorus in soil increased significantly with changes in above-ground organisms. Bacterial and fungal diversity responded differently to these changes, with bacterial community diversity varying significantly among different sites. Additionally, the settlement of embryogenic plants increased alpha-diversity indices in the soil, and certain bacterial phyla showed varying abundances based on the types of organisms covering the soil.
Article
Multidisciplinary Sciences
Guohuan Su, Maxime Logez, Jun Xu, Shengli Tao, Sebastien Villeger, Sebastien Brosse
Summary: A new study reveals significant changes in biodiversity in over half of the world's rivers, with human activities increasingly impacting freshwater fish. Current rivers show more similarity and a greater diversity of fish species, but face challenges such as the introduction of non-native species and river fragmentation.
Article
Agriculture, Multidisciplinary
Xiaotong Liu, Senwen Tan, Xiaojun Song, Xueping Wu, Gang Zhao, Shengping Li, Guopeng Liang
Summary: Global studies have shown that crop rotation can significantly increase soil organic carbon (SOC) content. The response of SOC content to crop rotation is influenced by climate, soil texture, and agronomic factors. The effect of crop rotation varies in different climate types, and neutral soils with loamy texture and appropriate initial SOC and total nitrogen levels are beneficial for increasing SOC content. Moreover, factors such as the number of rotation cycles, rotation length, nitrogen fertilization rate, and agronomic practices like no-till, straw retention, and organic fertilization also affect SOC content.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2022)
Article
Environmental Sciences
Yueqi Hao, Fubo Yu, Xiangang Hu
Summary: Soil microbial assemblages play a crucial role in biogeochemical cycling, and predicting ecological safety concerns requires consideration of multiple factors. The FEML approach can visualize the relationships among factors and predict changes in bacterial and fungal hotspots in the future. The imbalance between bacteria and fungi in soil ecosystems is significant, and mitigating climate change is essential to address this imbalance.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Soil Science
Zhibin Guo, Chang-An Liu, Keke Hua, Daozhong Wang, Shuixia Wan, Chuanlong He, Linchuan Zhan
Summary: This study investigates the impact of different cropland management systems on microbial diversity in soil during the transition period from winter to summer. The results show that bacteria and fungi respond differently to seasonal changes, and the changes in diversity between treatments do not sync with each other. The complex interaction between land management and sampling time affects bacterial diversity more than fungal diversity. It is suggested that assessing fungal diversity between management practices can be done without considering temporal variation.
Article
Plant Sciences
Yi Zhang, Yingzhong Xie, Hongbin Ma, Juan Zhang, Le Jing, Yutao Wang, Jianping Li
Summary: The study showed that increased precipitation promoted root growth in plants and the interaction of temperature and precipitation had a promoting effect on the diversity of fungi. In terms of bacteria, the diversity in the CK treatment was significantly higher than in other treatments.
Article
Ecology
Ziheng Peng, Yu Liu, Jiejun Qi, Hang Gao, Xiaomeng Li, Qi Tian, Xun Qian, Gehong Wei, Shuo Jiao
Summary: This study examined the distribution patterns and environmental drivers of fungal soil-borne pathogens in agricultural fields across China. It found that climate factors, such as temperature and precipitation, regulated the abundance and richness of these pathogens, with higher levels in the topsoil. The dominant pathogens were identified as two phylotypes belonging to the genus Fusarium, and their abundance was negatively correlated with precipitation and temperature. These findings have important implications for pathogen control and crop production.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Editorial Material
Multidisciplinary Sciences
Songhan Wang, Yongguang Zhang, Weimin Ju, Jing M. Chen, Alessandro Cescatti, Jordi Sardans, Ivan A. Janssens, Mousong Wu, Joseph A. Berry, J. Elliott Campbell, Marcos Fernandez-Martinez, Ramdane Alkama, Stephen Sitch, William K. Smith, Wenping Yuan, Wei He, Danica Lombardozzi, Markus Kautz, Dan Zhu, Sebastian Lienert, Etsushi Kato, Benjamin Poulter, Tanja G. M. Sanders, Inken Krueger, Rong Wang, Ning Zeng, Hanqin Tian, Nicolas Vuichard, Atul K. Jain, Andy Wiltshire, Daniel S. Goll, Josep Penuelas
Summary: Our study shows that the global CO2 fertilization effect on vegetation photosynthesis has decreased over the past four decades. Despite concerns raised in the Comments, additional evidence supports the robustness of our findings regarding the global decline in CFE.
Article
Ecology
Wesley A. Bickford, Deborah E. Goldberg, Donald R. Zak, Danielle S. Snow, Kurt P. Kowalski
Summary: The study found that there were no significant differences in the effects and responses of non-native and native Phragmites plants on soil microbes. Despite different treatments applied to the microbes, both lineages showed weak and insignificant plant-soil feedbacks.
ECOLOGICAL APPLICATIONS
(2022)
Article
Mycology
Kessy Abarenkov, Erik Kristiansson, Martin Ryberg, Sandra Nogal-Prata, Daniela Gomez-Martinez, Katrin Stueer-Patowsky, Tobias Jansson, Sergei Polme, Masoomeh Ghobad-Nejhad, Natalia Corcoll, Ruud Scharn, Marisol Sanchez-Garcia, Maryia Khomich, Christian Wurzbacher, R. Henrik Nilsson
Summary: The international DNA sequence databases contain many fungal sequences that are only annotated at the kingdom level, resulting in low-resolution mycological results and more poorly annotated entries. This study analyzes a dataset of 767,918 public full-length sequences to identify truly unidentifiable fungal taxa and determine the proportion of them that could have been easily identified at a higher taxonomic level. The findings suggest that over 70% of these sequences could have been identified at least to the order/family level at the time of sequence deposition, indicating that factors other than the availability of reference sequences contribute to the use of low-resolution names. The study also highlights the importance of addressing this problem, as a significant proportion of poorly annotated sequences are deposited by mycologists.
Article
Mycology
Chayanard Phukhamsakda, Rolf Henrik Nilsson, Chitrabhanu S. Bhunjun, Antonio Roberto Gomes de Farias, Ya-Ru Sun, Subodini N. Wijesinghe, Mubashar Raza, Dan-Feng Bao, Li Lu, Saowaluck Tibpromma, Wei Dong, Danushka S. Tennakoon, Xing-Guo Tian, Yin-Ru Xiong, Samantha C. Karunarathna, Lei Cai, Zong-Long Luo, Yong Wang, Ishara S. Manawasinghe, Erio Camporesi, Paul M. Kirk, Itthayakorn Promputtha, Chang-Hsin Kuo, Hong-Yan Su, Mingkwan Doilom, Yu Li, Yong-Ping Fu, Kevin D. Hyde
Summary: In this study, the diversity of fungi and the trends in species descriptions are examined based on 12 ascomycete genera. New species are introduced in each genus to emphasize the importance of traditional morpho-molecular methods. The relationship between the divergence times of these genera with those of their hosts is discussed, and the possibility of more species in these genera is hypothesized. The study also suggests hosts and habitats that should be investigated for novel species discovery.
Review
Biochemistry & Molecular Biology
Leho Tedersoo, Mohammad Bahram, Lucie Zinger, R. Henrik Nilsson, Peter G. Kennedy, Teng Yang, Sten Anslan, Vladimir Mikryukov
Summary: The development of high-throughput sequencing technologies has improved our ability to identify fungi and understand their ecological roles. This article provides an overview of the best practices in metabarcoding analysis of fungal communities, covering experimental design, molecular and computational analyses. The study shows that operational taxonomic units are more effective in recovering fungal diversity compared to amplified sequence variants, especially for long markers. Additionally, analyzing the full-length ITS region allows for more accurate taxonomic placement of fungi and other eukaryotes. The authors conclude that metabarcoding analyses of fungi have great potential for integrating fungi into the broader context of microbiome and ecosystem functioning.
Article
Biochemistry & Molecular Biology
Kadri Runnel, Kessy Abarenkov, Ovidiu Copot, Vladimir Mikryukov, Urmas Koljalg, Irja Saar, Leho Tedersoo
Summary: This study assessed the efficiency of long-read high throughput sequencing (HTS) for taxonomic identification of fungal specimens and found that PacBio HTS had a higher success rate and lower cost compared to Sanger sequencing. It also enabled the detection of gene polymorphism within the specimens, providing crucial information for species delimitation and population-level studies.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Mycology
Javier Isaac de la Fuente, Jesus Garcia-Jimenez, Tania Raymundo, Daniyal Gohar, Mohammad Bahram, Marcos Sanchez-Flores, Ricardo Valenzuela, Juan P. Pinzon
Summary: Two new species of Trichoglossum from south Mexico are described based on morphological and molecular evidence. They have distinct characteristics in ascomata, paraphyses, and ascospores, and both inhabit the tropical forests of the Yucatan peninsula.
Review
Clinical Neurology
Sven Kleine Bardenhorst, Emanuele Cereda, Marco Severgnini, Michela Barichella, Gianni Pezzoli, Ali Keshavarzian, Alessandro Desideri, Daniele Pietrucci, Velma T. E. Aho, Filip Scheperjans, Falk Hildebrand, Severin Weis, Markus Egert, Andre Karch, Marius Vital, Nicole Ruebsamen
Summary: The aim of this study is to reduce methodological heterogeneity in Parkinson's disease (PD) research and perform a pooled analysis. The results show that harmonizing workflows minimizes differences between statistical methods and reveals a small set of taxa associated with PD. Increased shares of Akkermansia and Bifidobacterium and decreased shares of Roseburia and Faecalibacterium are characteristic of PD-associated microbiota.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Microbiology
Clemence Frioux, Rebecca Ansorge, Ezgi Ozkurt, Chabname Ghassemi Nedjad, Joachim Fritscher, Christopher Quince, Sebastian M. Waszak, Falk Hildebrand
Summary: The composition of the human gut microbiome is usually in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states that are detrimental to host health. We have identified five generalizable enterosignatures dominated by different types of bacteria, which can be used to characterize the gut microbiome in health and disease. This model allows for the detection of gradual shifts in community structures and can reliably identify atypical gut microbiomes associated with adverse host health conditions and the presence of pathobionts.
CELL HOST & MICROBE
(2023)
Article
Environmental Sciences
Daniela Gomez-Martinez, Johanna Bengtson, Anders K. Nilsson, Adrian K. Clarke, Rolf Henrik Nilsson, Erik Kristiansson, Natalia Corcoll
Summary: Herbicide pollution is a global threat to plants and freshwater ecosystems. This study investigates how the green microalgal species Raphidocelis subcapitata adapts to the herbicide diflufenican and the associated trade-off expenses. The algae were exposed to diflufenican for 12 weeks and the results showed an initial dose-dependent stress phase, followed by a recovery phase. After acclimation, R. subcapitata exhibited similar growth, pigment composition, and photosynthetic performance as the unexposed algae, but with smaller cell size and changes in gene expression.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Mycology
R. Henrik Nilsson, Martin Ryberg, Christian Wurzbacher, Leho Tedersoo, Sten Anslan, Sergei Polme, Viacheslav Spirin, Vladimir Mikryukov, Sten Svantesson, Martin Hartmann, Charlotte Lennartsdotter, Pauline Belford, Maryia Khomich, Alice Retter, Natalia Corcoll, Daniela Gomez Martinez, Tobias Jansson, Masoomeh Ghobad-Nejhad, Duong Vu, Marisol Sanchez-Garcia, Erik Kristiansson, Kessy Abarenkov
Summary: Fungal metabarcoding reveals numerous fungal species that cannot be identified through morphology or cultivation. This challenges the current view that the situation is satisfactory and calls for discussion on DNA-based descriptions of species. The study proposes criteria for such descriptions.
Article
Biochemistry & Molecular Biology
Kessy Abarenkov, R. Henrik Nilsson, Karl-Henrik Larsson, Andy F. S. Taylor, Tom W. May, Tobias Guldberg Froslev, Julia Pawlowska, Bjoern Lindahl, Kadri Poldmaa, Camille Truong, Duong Vu, Tsuyoshi Hosoya, Tuula Niskanen, Timo Piirmann, Filipp Ivanov, Allan Zirk, Marko Peterson, Tanya E. Cheeke, Yui Ishigami, Arnold Tobias Jansson, Thomas Stjernegaard Jeppesen, Erik Kristiansson, Vladimir Mikryukov, Joseph T. Miller, Ryoko Oono, Francisco J. Ossandon, Joana Pauperio, Irja Saar, Dmitry Schigel, Ave Suija, Leho Tedersoo, Urmas Koljalg
Summary: UNITE is a web-based database and sequence management environment for molecular identification of eukaryotes. It offers a large number of sequences for reference and ensures accurate referencing through digital object identifiers. The latest release of UNITE has improved functionalities for biodiversity discovery and integration of biological knowledge.
NUCLEIC ACIDS RESEARCH
(2023)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Kessy Abarenkov, Anne Fouilloux, Helmut Neukirchen, Abdulrahman Azab
Summary: Reproducing eScience requires addressing several challenges such as automating scientific workflows, providing unambiguous software versions, easy access to input data, and enabling access to High-Performance Computing (HPC) clusters across borders for achieving bit-to-bit reproducibility. This paper presents a solution for accessing remote HPC and cloud compute and data resources from scientific portals across borders, through rigorous container-based packaging of software versions and setup automation, ultimately enhancing reproducibility.
2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022)
(2022)
Article
Microbiology
Julia Kleinteich, Kurt Hanselmann, Falk Hildebrand, Andreas Kappler, Christiane Zarfl
Summary: This study analyzed 16 lakes in the Eastern Swiss Alps and found that glacial melt-down alters the hydrological and physico-chemical conditions, leading to changes in sediment-associated microbial communities.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Biochemical Research Methods
Anna Pryszlak, Tobias Wenzel, Kiley West Seitz, Falk Hildebrand, Ece Kartal, Marco Raffaele Cosenza, Vladimir Benes, Peer Bork, Christoph A. Merten
Summary: We present a droplet microfluidic method for directly targeting and sorting individual cells from complex microbiome samples, enabling bulk whole-genome sequencing without the need for cultivation. This approach allows for the recovery of bacteria at low ratios and successful enrichment of specific strains for genome assembly. The encapsulation of microbiome samples in microfluidic droplets and the use of custom molecular probes facilitate the selective enrichment of target strains, addressing the lack of cultivated strains and reference genomes.
CELL REPORTS METHODS
(2022)
