Article
Microbiology
Diego Medina Caro, Lucas Horstmann, Lars Ganzert, Romulo Oses, Thomas Friedl, Dirk Wagner
Summary: Simultaneous extraction of intracellular DNA (iDNA) and extracellular DNA (eDNA) allows for separation of living in situ community (represented by iDNA) from background DNA. We tested different buffers with or without detergent mix (DM) to improve iDNA recovery. Sodium phosphate buffer plus DM significantly improved iDNA recovery, and sodium phosphate plus EDTA improved recovery and allowed extraction from low-biomass rock samples. We recommend a protocol with sodium phosphate and either DM or EDTA for iDNA extraction, and sodium phosphate only for eDNA extraction.
Article
Chemistry, Multidisciplinary
Lushun Wang, Chia-Heng Hsiung, Xiaojing Liu, Shichao Wang, Axel Loredo, Xin Zhang, Han Xiao
Summary: This study demonstrates the design and synthesis of a series of solvent-sensitive fluorophores that respond solely to polarity. These fluorophores can be used to detect protein aggregation in live cells and reveal polarity differences among different types of aggregates.
Article
Environmental Sciences
Shengcen Zhang, Binbin Xu, Mo Chen, Qianwen Zhang, Jiangqing Huang, Yingping Cao, Bin Li
Summary: The worldwide spread of carbapenem resistance genes (CRGs) is posing a major public health threat that is increasing in severity. Hospital wastewaters (HWWs) are significant reservoirs for antibiotic resistance genes, but the resistomes in HWWs, particularly CRGs, are not well characterized. This study comprehensively characterized the profile and transmissibility of extracellular and intracellular CRGs in HWWs for the first time.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Biotechnology & Applied Microbiology
Gavin Melaugh, Vincent A. Martinez, Perrin Baker, Preston J. Hill, P. Lynne Howell, Daniel J. Wozniak, Rosalind J. Allen
Summary: Researchers have found that Pseudomonas aeruginosa forms suspended multicellular aggregates in liquid media, and these aggregates may play important roles in disease and biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have been implicated in aggregation, but their roles vary depending on the growth stage of the bacterial cultures. Cell-associated Psl mediates aggregation in exponentially growing cultures, while both eDNA and Psl mediate cohesion in stationary phase cultures. These findings suggest that the properties of multicellular aggregates change throughout the growth cycle of P. aeruginosa.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Cell Biology
Laura K. Jennings, Julia E. Dreifus, Courtney Reichhardt, Kelly M. Storek, Patrick R. Secor, Daniel J. Wozniak, Katherine B. Hisert, Matthew R. Parsek
Summary: In cystic fibrosis airways, Pseudomonas aeruginosa forms biofilms that are thought to contribute to chronic infection. Exopolysaccharides Pel and Psi are expressed in CF airways and play a role in the aggregation mechanism, potentially impacting therapies by increasing antimicrobial tolerance and protecting extracellular DNA from digestion.
Article
Chemistry, Multidisciplinary
Mingqiang Ye, Yujing Kong, Cuiling Zhang, Yifei Lv, Shasha Cheng, Dongyan Hou, Yuezhong Xian
Summary: A NIR-photoactivatable DNA walker system powered by endogenous ATP was developed for in situ miRNA imaging in living cells with high spatial and temporal resolution. The system utilized UCNPs as carriers and transducers, showing stability and low fluorescent background. This smart system based on NIR light initiated DNA walker successfully achieved precise spatiotemporal control in living cells and has been applied for in situ miRNA imaging with high resolution.
Article
Environmental Sciences
Peiyuan Deng, Xiaojia Hu, Wentao Cai, Zuoxu Zhang, Yuli Zhang, Yihe Huang, Yingying Yang, Changkan Li, Shu Ai
Summary: The presence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) in the municipal wastewater treatment plant and its adjacent river sediments has been investigated. Results showed that internal DNA had higher absolute abundances of ARGs and MRGs compared to external DNA in the wastewater treatment plant, while the opposite was observed in river sediments. Aminoglycoside resistance genes were found to be the most abundant ARGs, while the zntA gene was one of the most abundant MRGs. The presence of the mobile genetic element intI1 was positively correlated with the proliferation of resistance genes in both internal and external DNA. This widespread distribution of ARGs, MRGs, and MGEs provides insights into the transmission routes and highlights the importance of monitoring and mitigating their dissemination.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Oncology
Ai Nakaoka, Makiko Nakahana, Sachiko Inubushi, Hiroaki Akasaka, Mohammed Salah, Yoshiko Fujita, Hikaru Kubota, Mennaallah Hassan, Ryo Nishikawa, Naritoshi Mukumoto, Takeaki Ishihara, Daisuke Miyawaki, Takashi Sasayama, Ryohei Sasaki
Summary: This study demonstrated that irradiated exosomes enhance the radiation effect by increasing intracellular ROS levels in cancer cells, contributing to a better understanding of the bystander effect of neighboring cancer cells.
Article
Biochemistry & Molecular Biology
Wendelin Dailey, Roberto Shunemann, Fang Yang, Megan Moore, Austen Knapp, Peter Chen, Mrinalini Deshpande, Brandon Metcalf, Quentin Tompkins, Alvaro E. Guzman, Jennifer Felisky, Kenneth P. Mitton
Summary: The study reveals that in primary human retinal microvascular endothelial cells, the VEGFA(165)a isoform can maximally activate MAPK and AKT at lower concentrations and have a greater impact on the expression of various VEGFA(165) target genes.
Article
Materials Science, Biomaterials
Zhe Zhang, Weiwei Tang, Yufeng Li, Yue Cao, Yuanhong Shang
Summary: By utilizing conjugated tri-porphyrins with absorption within a biological phototherapy window and bioinspired intracellular pH-sensitive metallo-supramolecular nanoparticles (NPs), simultaneous photothermal therapy and chemotherapy were achieved, leading to complete and recurrence-free relief of tumors in a 27-day course. These bioinspired intracellular pH-sensitive metallo-supramolecular NPs show excellent potential for near-infrared photoacoustic imaging-guided chemo-photothermal combined therapy.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2021)
Article
Soil Science
Shamina I. Pathan, Maria Teresa Ceccherini, Martin Asser Hansen, Laura Giagnoni, Judith Ascher, Mariarita Arenella, Soren J. Sorensen, Giacomo Pietramellara, Paolo Nannipieri, Giancarlo Renella
BIOLOGY AND FERTILITY OF SOILS
(2015)
Article
Soil Science
Shamina Imran Pathan, Lucia Zifcakova, Maria Teresa Ceccherini, Ottorino Luca Pantani, Tomas Vetrovsky, Petr Baldrian
SOIL BIOLOGY & BIOCHEMISTRY
(2017)
Article
Green & Sustainable Science & Technology
Gulab Singh Yadav, Rahul Datta, Shamina Imran Pathan, Rattan Lal, Ram Swaroop Meena, Subhash Babu, Anup Das, S. N. Bhowmik, Mrinmoy Datta, Poulami Saha, Pawan Kumar Mishra
Article
Agronomy
Shamina Imran Pathan, Tomas Vetrovsky, Laura Giagnoni, Rahul Datta, Petr Baldrian, Paolo Nannipieri, Giancarlo Renella
Article
Multidisciplinary Sciences
Shamina Imran Pathan, Paola Arfaioli, Maria Teresa Ceccherini, Judith Ascher-Jenull, Giacomo Pietramellara
Article
Agriculture, Multidisciplinary
Giuseppe Badagliacca, Beatrix Petrovicova, Shamina Imran Pathan, Angela Roccotelli, Maurizio Romeo, Michele Monti, Antonio Gelsomino
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2020)
Article
Soil Science
Shamina Imran Pathan, Angela Roccotelli, Beatrix Petrovicova, Maurizio Romeo, Giuseppe Badagliacca, Michele Monti, Antonio Gelsomino
Summary: A field experiment was conducted in tree orchard soils in Southern Italy to investigate the impact of two improved tillage systems on the prokaryotic community composition. The study found that soil management induced compositional shifts in the microbial community balance, with different responses observed based on soil type and treatment, affecting both abundance and diversity of the prokaryotic communities.
BIOLOGY AND FERTILITY OF SOILS
(2021)
Review
Biology
Giacomo Pietramellara, Shamina Imran Pathan, Rahul Datta, Valerie Vranova, MariaTeresa Ceccherini, Paolo Nannipieri
Summary: This paper discusses the challenges of determining the presence and impact of SARS-CoV-2 in soil, focusing on its adsorption, movement, and infectivity mechanisms. Future research should focus on plant uptake, virus adsorption and desorption in soil, and the effects on soil functions. Models should be developed to simulate the spatial localization of the virus in the soil.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Soil Science
Margherita Santoni, Leonardo Verdi, Shamina Imran Pathan, Marco Napoli, Anna Dalla Marta, Francesca Romana Dani, Gaio Cesare Pacini, Maria Teresa Ceccherini
Summary: This study compared the effects of organic and conventional farming systems on microbial biomass, activity, soil CO2 emission, and available nitrogen forms. The results showed that organic farming had more active and abundant microbial biomass, with fungi being more active than bacteria. Organic farming also had higher bacterial richness and lower levels of NO3-.
SOIL USE AND MANAGEMENT
(2023)
Article
Environmental Studies
Tommaso Bardelli, Shamina Imran Pathan, Paola Arfaioli, Nadia Vignozzi, Sergio Pellegrini, Flavio Fornasier, Markus Egli, Maria Gomez-Brandon, Heribert Insam, Giacomo Pietramellara, Judith Ascher-Jenull
Summary: This study evaluated the effects of slope exposure on the physico-chemical and microbiological properties of soil in an Italian alpine forest. The results showed that slope exposure significantly influenced soil properties and enzyme activities. The effects varied between north-facing and south-facing slopes, as well as among soil horizons and aggregate size fractions.
Article
Microbiology
Shamina Imran Pathan, Paola Arfaioli, Eren Taskin, Maria Teresa Ceccherini, Edoardo Puglisi, Giacomo Pietramellara
Summary: Environmental DNA is composed of intracellular (iDNA) and extracellular (eDNA) pools, with eDNA potentially distorting assessments of living microorganisms in soils. The distribution of microbial communities varies among different size-aggregates, and the uneven persistence and turnover of eDNA may cause biases in community analysis. Therefore, understanding the presence and impact of eDNA is important for accurate assessment of soil microbial communities.
FEMS MICROBIOLOGY LETTERS
(2021)
Review
Environmental Studies
Ram Swaroop Meena, Sandeep Kumar, Rahul Datta, Rattan Lal, Vinod Vijayakumar, Martin Brtnicky, Mahaveer Prasad Sharma, Gulab Singh Yadav, Manoj Kumar Jhariya, Chetan Kumar Jangir, Shamina Imran Pathan, Tereza Dokulilova, Vaclav Pecina, Theodore Danso Marfo
Article
Biodiversity Conservation
Theodore Danso Marfo, Rahul Datta, Shamina Imran Pathan, Valerie Vranova
Review
Agronomy
Rahul Datta, Swati Anand, Amitava Moulick, Divyashri Baraniya, Shamina Imran Pathan, Klement Rejsek, Valerie Vranova, Meenakshi Sharma, Daisy Sharma, Aditi Kelkar, Pavel Formanek
INTERNATIONAL AGROPHYSICS
(2017)
Article
Soil Science
He Zhang, Aurore Degre, Caroline De Clerck, Shuangshuang Li, Jinshan Lian, Yuanyuan Peng, Tao Sun, Lindan Luo, Yanan Yue, Guihua Li, Jianfeng Zhang
Summary: The continuous expansion of sandy soil poses a threat to crop security. The use of chitin-rich organic material and attapulgite as soil amendments can improve degraded soil by increasing nutrient content and enzyme activity and altering bacterial community structure. This study provides insights into the link between soil properties, bacterial community structure, and microbial carbon metabolism function.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Xian Zhou, Yi Jiang, Ganghua Leng, Wanting Ling, Jian Wang
Summary: Bound Polycyclic Aromatic Hydrocarbons (PAHs) residues have significant impacts on soil pollution remediation. The addition of exogenous functional microbial consortium and glomalin-related soil protein (GRSP) can promote the degradation of bound PAH residues. This study fills the cognitive gap of GRSP in regulating the degradation of bound PAH residues in soil.
APPLIED SOIL ECOLOGY
(2024)
Review
Soil Science
Xinyu Zhao, Evrim Elcin, Lizhi He, Meththika Vithanage, Xiaokai Zhang, Jie Wang, Shuo Wang, Yun Deng, Nabeel Khan Niazi, Sabry M. Shaheen, Hailong Wang, Zhenyu Wang
Summary: The increase of cultivated varieties of Chinese herbal remedies, the expansion of cultivation area, and long-term monoculture cropping have led to aggravated problems of soil diseases, yield loss, and quality reduction. Biochar, as a carbon-rich material, has the potential to improve soil quality and alleviate continuous crop obstacles for Chinese herbal remedies.
APPLIED SOIL ECOLOGY
(2024)
Editorial Material
Soil Science
Melanie M. Pollierer, Anton Potapov, Andrey Zaitsev
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Yajie Wang, Jiefeng Li, Yongfen Wei, Zhiyi Deng, Xiaodi Hao, Fusheng Li
Summary: This study investigates the impacts of heavy metal pollution caused by coal production on soil microbial ecology in the semi-arid region of Heilongjiang. The results reveal negative correlations between heavy metals and bacterial abundance and diversity. Twelve sensitive bacterial taxa and corresponding models were identified. Water content and total phosphorus were also found to play vital roles in regulating the bacterial community in the soil.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Sujit Das, Sunanda Biswas, B. Ramakrishnan, T. K. Das, T. J. Purakayastha, B. H. Gawade, Priya Singh, Partha Sarathi Ghorai, Saloni Tripathy, Kanchan Sinha
Summary: This study assessed the impact of conservation agriculture on the biological soil health index in a rice-wheat system in the Indo-Gangetic Plains. The results showed that zero till direct seeded rice and crop residue incorporation could improve soil organic carbon, enzyme activities, and microbial population. Specifically, the inclusion of mungbean residues and sesbania brown manuring significantly increased the abundance of the nifH gene in the soil.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Xingxiu Huang, Genxing Pan, Lianqing Li, Xuhui Zhang, Hailong Wang, Nanthi Bolan, Bhupinder Pal Singh, Chongjian Ma, Fuwei Liang, Yanjie Chen, Huashou Li
Summary: The study evaluated the effects of using a mixture of biomass waste ash and biochar on soil pH, heavy metal remediation, and plant growth. The results showed that the mixed use could ameliorate soil acidification, reduce absorption of cadmium and lead by plants, and promote plant growth. The special fertilizer prepared from the mixture can be used to promote crop growth and reduce environmental pollution.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Astrid C. H. Jaeger, Martin Hartmann, Rafaela Feola Conz, Johan Six, Emily F. Solly
Summary: This study investigates the effects of tree mortality on soil microbial communities using a mesocosm experiment. The results show that tree death influenced soil microbial abundance and composition, with the potential to affect soil processes in forest ecosystems.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Dane C. Elmquist, Subodh Adhikari, Ina Popova, Sanford D. Eigenbrode
Summary: This study investigated the effects of soil arthropod communities from cereal-based agroecosystems on wheat plant growth and above-belowground interactions. The results showed that wheat grown in soils with arthropod communities had better growth and defense against aphids, compared to wheat grown in soils without arthropod communities.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Lei Wang, Jing Wang, Zhonghou Tang, Jidong Wang, Yongchun Zhang
Summary: This study found that the application of organic fertilizer enhances carbon and phosphorus cycling enzyme activities in soil, reshapes the soil microbial community structure, and regulates the interactions between these crucial indicators through soil organic carbon.
APPLIED SOIL ECOLOGY
(2024)
Review
Soil Science
M. Pawlett, N. T. Girkin, L. Deeks, D. L. Evans, R. Sakrabani, P. Masters, K. Garnett, N. Marquez-Grant
Summary: The modern funeral industry faces environmental risks and challenges, and natural burial offers a more sustainable alternative. However, there is a lack of research comparing the risks and benefits of natural burial practices, including groundwater contamination and atmospheric emissions. More scientific research is needed to understand and regulate funeral options, as well as cultural incentives for natural burial.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Zhongcheng Wang, Jin Zhao, Dan Xiao, Meifeng Chen, Xunyang He
Summary: Root AMF colonization, diversity, and interactions vary with soil depth. Higher soil nutrient levels and root biomass promote colonization but suppress diversity and interactions in the upper soil layer compared to deeper layers.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Zhiyang Zhang, Shiting Zhang, Riikka Rinnan
Summary: This study revealed the mechanisms behind the effects of dung deposition on soil heterotrophic respiration, providing insights for grassland management and carbon feedback prediction in grazed ecosystems.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Ismail Ibrahim Garba, Graham R. Stirling, A. Marcelle Stirling, Alwyn Williams
Summary: Integrating diverse cover crops into dryland crop-fallow rotations can enhance soil nutrient and water retention, suppress soil-borne pests, and improve soil health. The effects on soil nematode communities are modulated by the functional type and mixture composition of the cover crops. Selecting cover crops with appropriate traits can improve soil health through suppression of plant-parasitic nematodes, promotion of free-living nematodes, and enhancement of soil food web complexity.
APPLIED SOIL ECOLOGY
(2024)
Article
Soil Science
Min Li, Chao He, Miao Wei, Junmeng Long, Jingru Wang, Xinrong Yang, Kehan Wang, Xueli He
Summary: In extreme desert environments, black septate endophytes (DSE) can benefit the relict plant Gymnocarpos przewalskii by assisting it to survive and maintain ecosystem stability. The colonization of DSE in the roots of G. przewalskii varies significantly with seasons and sites, with soil properties being a major factor affecting the composition of DSE. Additionally, the functional metabolite composition of DSE strains varies greatly with different drought levels and isolates, indicating the potential complementarity between different strains in helping hosts cope with drought stress.
APPLIED SOIL ECOLOGY
(2024)