Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Infectious Diseases
Simon Hosbond Poulsen, Kirstine Kobberoe Sogaard, Kurt Fuursted, Hans Linde Nielsen
Summary: This study retrospectively evaluated the diagnostic accuracy and clinical utility of 16S/18S tNGS in the routine clinical setting. The results showed that tNGS had a certain sensitivity and specificity for detecting pathogenic microorganisms and could detect a greater variety of bacteria and fungi. However, the long turnaround time of tNGS and limited impact on clinical management were observed.
INFECTIOUS DISEASES
(2023)
Article
Environmental Sciences
Thuy Tram Nguyen, Thi Trang Le, Huy Hoang Le, Thi Nga Tang, Thi Thu Hang Phung, Thi Mai Hien Vu, Thi Hai Au Tran, Dong Tu Nguyen, Thi Phuong Lien Nguyen, Duc Phuc Pham, Panagiotis Karanis
Summary: This study aimed to investigate the presence of Cryptosporidium and Giardia in environmental samples and fecal samples of biogas users in Bac Giang province, Vietnam. The results showed that a small percentage of samples tested positive for Cryptosporidium oocysts and Giardia cysts. The presence of certain genotypes and assemblages of these protozoa were identified, including some that were previously unknown in humans in Bac Giang.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Article
Food Science & Technology
Celia Carbonne, Karine Labadie, Corinne Cruaud, Elodie Brun, Valerie Barbe, Christophe Monnet
Summary: This study evaluated the efficiency of RNA extraction from different types of cheeses and the impact of mRNA enrichment methods on metatranscriptomic analyses. The results showed variations in RNA yield and integrity among different cheese types, as well as differences in the impact of mRNA enrichment methods on gene expression profiles. These findings are important for metatranscriptomic analysis of cheeses.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Article
Environmental Sciences
R. G. Bulgarelli, M. F. A. Leite, M. De Hollander, P. Mazzafera, S. A. L. Andrade, E. E. Kuramae
Summary: The availability of soil phosphorus can affect plant growth, root-soil interactions, and rhizosphere microbial community composition. This study investigated the rhizosphere microbial communities of 24 species of eucalypts under low or sufficient soil phosphorus availability. It was found that eucalypt species identity was the main factor determining the composition of the rhizosphere microbial community, while the effect of phosphorus availability varied among species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Plant Sciences
Micaela Tosi, Cameron M. Ogilvie, Federico N. Spagnoletti, Sarah Fournier, Ralph C. Martin, Kari E. Dunfield
Summary: Cover crops improve soil health and water supply for cash crops, but their effects on plant-associated microbial communities, including AMF, are unclear.
Article
Biodiversity Conservation
Anais Chanson, Corrie S. Moreau, Christophe Duplais
Summary: This study examines the impact of host ecology and evolutionary history on the microbial communities of Amazonian ants. The research shows that habitat does not play a role in structuring ant microbial communities, but ant diet and nesting mode do influence bacterial communities. Additionally, nesting mode is the determining factor for microbial eukaryote communities, while microbial diversity is not correlated with host phylogeny.
Article
Agriculture, Dairy & Animal Science
Nyaradzo Stella Chaora, Khulekani Sedwell Khanyile, Kudakwashe Magwedere, Rian Pierneef, Frederick Tawi Tabit, Farai Catherine Muchadeyi
Summary: This study utilized gene sequencing and bioinformatics analysis to determine mislabeling of processed meat products using the mitochondrial 16S ribosomal RNA gene. The results showed that pork was the major contaminant in most meat samples. This method can be used to authenticate meat products and manage mislabeling.
Article
Veterinary Sciences
Liheng Zhang, Xianghui Li, Xinghui Song, Chuanzhou Bian, Xiangtao Kang, Junqiang Zhao, Hongxing Qiao, Yanzhang Gong
Summary: Endophytic fungi are microorganisms that exist within healthy plant organs and have a significant influence on the production of metabolic products in plants. Fermentation with probiotic cultures can affect the diversity and abundance of endophytic fungi in Astragalus membranaceus. These findings provide a foundation for exploring the potential use of endophytic fungi from A. membranaceus as a source of functional compounds.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Engineering, Environmental
Paula Maza-Marquez, Alejandro Rodriguez-Sanchez, Barbara Munoz-Palazon, Jesus Gonzalez-Lopez, Alejandro Gonzalez-Martinez
Summary: Next-generation sequencing and metatranscriptomic analysis were used to study the microbial diversity and gene mechanisms in a cold bioreactor treating urban wastewater near the Polar Arctic Circle. Several cold adaptation mechanisms and genes related to drug and heavy metal resistance were identified, indicating the presence of functional diversity in cold environments.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Anastasija Zaiko, Paul Greenfield, Cathryn Abbott, Ulla von Ammon, Jaret Bilewitch, Michael Bunce, Melania E. Cristescu, Anthony Chariton, Eddy Dowle, Jonathan Geller, Alba Ardura Gutierrez, Mehrdad Hajibabaei, Emmet Haggard, Graeme J. Inglis, Shane D. Lavery, Aurelija Samuiloviene, Tiffany Simpson, Michael Stat, Sarah Stephenson, Judy Sutherland, Vibha Thakur, Kristen Westfall, Susanna A. Wood, Michael Wright, Guang Zhang, Xavier Pochon
Summary: Advances in high-throughput sequencing technology are changing marine monitoring by enabling rapid and accurate detection of species in complex samples. An international experiment showed that while there was variation in results from different laboratories, the primary signal in the data was consistent, with samples grouping by geographical origin. Post hoc data clean-up, such as removing low-quality samples, improved sample classification accuracy significantly.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Pediatrics
Yi-Sheng Chang, Chang-Wei Li, Ling Chen, Xing-An Wang, Maw-Sheng Lee, Yu-Hua Chao
Summary: The development of the gut microbiome during early life has long-term effects on health. This study analyzed the microbiota profile of the first-pass meconium in healthy neonates and found a similar composition, with Pseudomonas being the most abundant genus. The diversity of the microbial communities in the first-pass meconium was extremely poor. Primigravidae babies had a higher diversity index, and the Bacteroidales order was a biomarker for their meconium. Delivery mode, maternal antibiotic treatment, rupture of membranes, and birth weight did not affect the diversity index.
Article
Microbiology
Shan Jiang, Saisai Lu, Xiaomin Chen, Fengxia Li, Chengwei Zhu, Yuancai Zheng, Xiaobing Wang, Shihao Xu
Summary: This study identified distinct urine microbial features in patients with obstructive urinary retention caused by urinary stones or urinary tract tumors compared to healthy controls. Despite different origins, similarities in urine microbial community and functional characteristics were observed in both types of UR, allowing for accurate classification using specific enriched bacterial genera.
ANNALS OF CLINICAL MICROBIOLOGY AND ANTIMICROBIALS
(2021)
Article
Microbiology
Peeter Laas, Kelly Ugarelli, Rafael Travieso, Sandro Stumpf, Evelyn E. Gaiser, John S. Kominoski, Ulrich Stingl
Summary: Planktonic microbial communities in wetland ecosystems play a vital role, yet they are relatively underexplored compared to other aquatic ecosystems. This study conducted a high-resolution analysis of bacterial and eukaryotic microbial communities in the Florida Everglades, revealing significant variations along the salinity gradient.
Article
Environmental Sciences
Guangquan Chen, Shiyi Xiong, Qiao Jing, Cornelis A. M. van Gestel, Nico M. van Straalen, Dick Roelofs, Luming Sun, Hao Qiu
Summary: This study investigated the effects of polystyrene nanoplastics (PS-NPs) on fetal development and cholesterol metabolism in mice. The exposure to PS-NPs led to a decline in fetal weights and abnormal cell morphologies in the placenta and fetus. Transcriptomic and metabolomic analyses revealed disturbances in cholesterol metabolism and other pathways, offering new insights into the mechanisms underlying the detrimental effects of PS-NPs on placenta and fetus.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Soil Science
Zhikang Wang, Marcio F. A. Leite, Mingkai Jiang, Eiko E. Kuramae, Xiangxiang Fu
Summary: Periodic inoculations of soil-beneficial microbes increase their populations but also act as recurring biotic disturbances on the native microbial community. Rare and abundant microorganisms disproportionately shape community diversity and stability. Understanding their dynamic responses and driving factors helps improve our understanding of inoculation effects.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Soil Science
Lv Su, Huatai Li, Jing Wang, Wenting Gao, Xia Shu, Xiting Sun, Kesu Wang, Yan Duan, Yunpeng Liu, Eiko E. Kuramae, Ruifu Zhang, Biao Shen
Summary: Bacteria that dominate and become enriched in the rhizosphere during continuous cropping have attracted increasing interest due to their ability to adapt well to the rhizosphere. However, little is known about their general composition and function. In this study, we conducted high-throughput sequencing and culture-dependent workflows to investigate the composition and function of rhizosphere bacteria during continuous cropping of tomatoes in different soils. We observed a similar succession of bacterial community compositions in the rhizosphere, and identified certain bacteria that were gradually enriched and potentially beneficial. Our study also revealed the enrichment of predicted functions related to xenobiotic biodegradation, nutrient metabolism, and antibiotic biosynthesis in different rhizosphere soils. We further demonstrated the inhibitory effect of Beijerinckia fluminensis GR2, which was gradually enriched in all tested soils, on the growth of Ralstonia solanacearum and its protective role against infection. These findings provide new insights into the assembly mechanism of gradually enriched bacteria and their role as plant-beneficial microbes in the rhizosphere.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Environmental Sciences
Dik van de Meent, Dick de Zwart, Jaap Struijs, Joop L. M. Hermens, Nico M. van Straalen, Klaas H. den Haan, John R. Parsons, Pim de Voogt, Kees van Leeuwen
Summary: This paper presents a simple modeling procedure to calculate the 'expected risk' (ER) of chemical substances. The procedure combines multimedia environmental fate modeling and species sensitivity modeling to determine the probability of exposure concentrations exceeding critical effect concentrations. The study found that the ER and Risk Quotient (RQ) of chemicals can be easily calculated and used to assess environmental safety and rank chemicals accordingly. The paper suggests that modeling ER instead of estimating RQ values could enhance the scientific basis of environmental risk assessment in REACH, and recommends the use of acute EC50 as the critical effect concentration for more robust risk calculation.
ENVIRONMENTAL SCIENCES EUROPE
(2023)
Article
Soil Science
Ohana Y. A. Costa, Agata Pijl, Jos Houbraken, Willem van Lith, Eiko E. Kuramae
Summary: Plant biostimulants, including gelatin, can enhance plant nutrition processes and nutrient uptake efficiency by stimulating the growth of beneficial soil microbes. In this study, the effects of gelatin on microbial communities in different soils and substrates were investigated using high-throughput sequencing. The results showed that gelatin amendment positively impacted the abundance of certain fungal and bacterial genera, indicating potential for formulating beneficial microbial consortia to enhance its biostimulant activity.
APPLIED SOIL ECOLOGY
(2023)
Article
Soil Science
Lv Su, Huatai Li, Xiting Sun, Kesu Wang, Xia Shu, Wenting Gao, Yunpeng Liu, Eiko E. Kuramae, Biao Shen, Ruifu Zhang
Summary: Phenolic acids, released from plant residue decomposition, have significant effects on the soil microbiome. The study examined the impact of four phenolic acids on soil fungal communities and found that they increased the deterministic assembly process but decreased fungal diversity. Salicylic acid had the greatest impact and certain fungal species were enriched at high concentrations. These findings enhance our understanding of fungal assembly and aid in identifying phenolic acid-degrading microbes.
APPLIED SOIL ECOLOGY
(2023)
Article
Agricultural Engineering
Yingxin Li, Eiko E. Kuramae, Fahad Nasir, Enze Wang, Zhengang Zhang, Ji Li, Zongmu Yao, Lei Tian, Yu Sun, Shouyang Luo, Lingling Guo, Gaidi Ren, Chunjie Tian
Summary: To improve the decomposition of cellulose, cellulose-degrading bacteria were added, which successfully enhanced the degradation ability and promoted the growth of fungi.
BIORESOURCE TECHNOLOGY
(2023)
Article
Agronomy
Joao William Bossolani, Carlos Alexandre Costa Crusciol, Eduardo Mariano, Mariley Fonseca, Luiz Gustavo Moretti, Letusa Momesso, Jose Roberto Portugal, Nidia Raquel Costa, Juliano Carlos Calonego, Eiko Eurya Kuramae
Summary: The application of lime and phosphogypsum on the surface in no-tillage rotation systems can improve soil fertility and increase the recovery of nitrogen fertilizer, resulting in higher grain yield. The abundance of microbial genes and crop yield are closely related to agricultural management practices.
EUROPEAN JOURNAL OF AGRONOMY
(2023)
Article
Soil Science
Akari Mitsuta, Nao Ishige, Chikae Tatsumi, Yvonne Musavi Madegwa, Eiko Eurya Kuramae, Yoshitaka Uchida
Summary: The diversity of soil microbial community plays a crucial role in the stability of ammonia-oxidizing bacteria and archaea, especially in the presence of repeated nitrogen fertilization in agricultural systems.
Article
Plant Sciences
S. Franz Bender, Stefanie Schulz, Ruben Martinez-Cuesta, Ronald J. Laughlin, Susanne Kublik, Kristina Pfeiffer-Zakharova, Gisle Vestergaard, Kyle Hartman, Eloi Parlade, Jorg Rombke, Catherine J. Watson, Michael Schloter, Marcel G. A. van Der Heijden
Summary: Agriculture is a major contributor to nutrient pollution, but the potential of soil biota to improve nutrient cycling and reduce losses is not well understood. This study found that simplified soil biota communities led to decreased nutrient uptake, increased nutrient losses, and higher gas emissions. Soil metagenomic analysis helped explain these findings.
Article
Environmental Sciences
Joao W. Bossolani, Marcio F. A. Leite, Letusa Momesso, Hein Ten Berge, Jaap Bloem, Eiko E. Kuramae
Summary: The challenges of nitrogen management in agriculture include maximizing profits and soil health while minimizing nitrogen losses. Organic amendments with different carbon-to-nitrogen ratios can modify soil bacteria and microbial activity, affecting carbon and nitrogen cycling processes. High carbon-to-nitrogen ratio amendments had the strongest impact on soil carbon extraction, microbial biomass, and respiration, while low carbon-to-nitrogen ratio amendments had a greater effect on nitrogen transformation processes. Incorporating mineral nitrogen management is crucial, especially when using high carbon-to-nitrogen ratio amendments, to achieve higher crop yields.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Soil Science
Li Ji, Chunjie Tian, Eiko E. Kuramae
Summary: This study explored the relationship between microbial functions and soil element turnover during rice cultivation in saline-alkali soil over varying durations. The results showed that rice cultivation greatly improved soil nutrients, soil nutrient stoichiometry, and soil aggregate stability. It also enhanced the microbial functions involved in nutrient cycling, but these functions exhibited a succession pattern with the years of remediation. Correlation analysis indicated that soil microbial functions were closely related to changes in soil properties, especially phosphorus availability. Therefore, managing phosphorus during saline-alkali soil remediation should be prioritized.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Forestry
Buck T. Castillo, Rima B. Franklin, Kevin R. Amses, Marcio F. A. Leite, Eiko E. Kuramae, Christopher M. Gough, Timothy Y. James, Lewis Faller, John Syring
Summary: The study found that fungal communities play a crucial role in the decomposition of detritus, including coarse woody debris. Fungal communities rapidly colonize dead trees and gradually change in composition until the late stages of decomposition, during which decomposed wood is integrated into soil organic matter. Fungal communities show similarity with neighboring stages of decay and are positively related to nitrogen content. Enzyme activity changes mirror differences in carbon recalcitrance, with enzymes increasing as decomposition progresses. Fungal and bacterial gene abundances remain stable and increase, respectively, with the extent of decay.
Article
Environmental Sciences
Shuaimin Chen, Eiko E. Kuramae, Zhongjun Jia, Binbin Liu
Summary: This study utilized stable isotope probing and molecular biology techniques to investigate the composition and function of active denitrifying microorganisms in the vadose zone. It revealed significant differences in the composition and function of active denitrifiers between different soil layers. This research improves our understanding of active denitrifying microbes in the vadose zone and provides insights for reducing nitrate pollution in groundwater.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Ecology
Menghui Dong, Eiko E. Kuramae, Mengli Zhao, Rong Li, Qirong Shen, George A. Kowalchuk
Summary: In this study, we investigated the impact of tomato plants on soil aggregation and bacterial communities within different soil aggregate size classes. Our results showed that the development stages of tomato plants negatively affected root-adhering soil aggregation and resulted in changes in bacterial density and community composition, which varied across soil aggregate size classes. Additionally, we found that plant pathogens exhibited a preference for micro-aggregates, while macro-aggregates held a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes.
ISME COMMUNICATIONS
(2023)