Article
Microbiology
Kara A. Tinker, Elizabeth A. Ottesen
Summary: The gut microbiome composition in cockroaches is influenced by host genetics, founder's effects, and host environment. Using cockroaches as a model, this study found that the gut microbiome differs by both species and rearing environment. Transition to a laboratory environment decreased microbiome diversity for both species of wild-caught insects.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Xiaodan Li, Songfeng Wang, Yating Fan, Zhe Zhou, Sheng Xu, Penglei Zhou, Jiayu Zhou, Ren Wang
Summary: This study investigates the impact of peanut rotation and flooding on the growth and yield of Corydalis yanhusuo. The results suggest that the altered soil physicochemical properties caused by these practices could lead to changes in the rhizobacteriome of C. yanhusuo, ultimately affecting its growth and medicinal yield.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Environmental Sciences
Kusum Dhakar, Shlomit Medina, Hamam Ziadna, Karam Igbaria, Guy Achdari, Ran Lati, Raphy Zarecki, Zeev Ronen, Guy Dovrat, Hanan Eizenberg, Shiri Freilich
Summary: Microbial communities in different crop fields respond differently to the application of the herbicide atrazine, as revealed by 16S rRNA gene amplicon sequencing. The nutrient-poor soil showed a different response compared to the nutrient-rich soils, both in terms of atrazine persistence and its effect on bacterial community structure and composition. Specific bacterial degraders of atrazine were more abundant in the contaminated nutrient-poor soil, while bacteria involved in nitrogen cycling were more abundant in the contaminated nutrient-rich soil. Understanding these responses can help in designing precision application strategies.
ENVIRONMENTAL RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Marcel Suleiman, Francesca Demaria, Cristina Zimmardi, Boris Alexander Kolvenbach, Philippe Francois-Xavier Corvini
Summary: Pharmaceuticals accumulation in the environment is a concern for our planet and health. Little is known about the biodegradation capacity of microbial communities for multiple micropollutants. This study demonstrates the feasibility of cultivating stable microbial communities capable of degrading a mixture of highly concentrated pharmaceuticals.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Food Science & Technology
Jaana Huotari, Irina Tsitko, Kaisu Honkapaa, Hanna-Leena Alakomi
Summary: There is growing interest in using whole Baltic herring for food consumption and this study explored the suitability of ungutted herring for this purpose. The microbiological quality of commercially fished whole and gutted herring was analyzed, and it was found that the bacterial diversity was good and the microbiological quality was acceptable in all the analyzed fish batches.
Article
Microbiology
Ezgi Ozkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
Summary: LotuS2 is a lightweight and user-friendly pipeline for amplicon sequence analysis, offering high speed and precision, as well as improved data quality through extensive pre- and post-processing steps.
Article
Microbiology
Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Summary: This study reanalyzed data from a large sample storage study, confirming that 95% ethanol is an effective, practical, and cost-effective preservative that can preserve samples at room temperature for weeks. It also identified the optimal ratio of 95% ethanol to sample in stool and saliva samples, providing a solution that enables crowdsourcing microbiome studies and lowers the barrier for collecting diverse samples.
Article
Biotechnology & Applied Microbiology
Dong Han, Hongmin Zhen, Xiaoyan Liu, Justyna Zulewska, Zhennai Yang
Summary: This study used both rRNA and gDNA sequencing on mouse cecal contents and found differences in microbial composition and functional predictions between the two methods. rRNA-derived sequencing improved identification capability of specific microorganisms and was more suitable for functional predictions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Jonas Greve Lauritsen, Morten Lindqvist Hansen, Pernille Kjersgaard Bech, Lars Jelsbak, Lone Gram, Mikael Lenz Strube
Summary: A high-throughput sequencing method was developed for profiling Pseudomonas species in soil microbiomes, identifying more species than 16S rRNA gene sequencing or cultivation. This method allows for tracing specific species of Pseudomonas and screening environmental samples for further isolation and exploitation.
Article
Immunology
Kelvin Li, Barbara A. Methe, Adam Fitch, Heather Gentry, Cathy Kessinger, Asha Patel, Vickie Petraglia, Pruthvi Swamy, Alison Morris
Summary: Imposition of social and health behavior measures during the COVID-19 pandemic may impact the human microbiota, but further research is needed to confirm this hypothesis. This study found that while there was a trend of reduced diversity, the microbiota remained stable overall during the early pandemic phase. Changes in microbiota composition were associated with reported health issues and pandemic-associated worries.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Agriculture, Dairy & Animal Science
Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramirez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Summary: Microbiome studies in animal science using 16S rRNA gene sequencing are becoming more common. This review serves as a guide for animal scientists less familiar with this method, discussing common issues and considerations in planning such studies.
JOURNAL OF ANIMAL SCIENCE
(2022)
Review
Biochemical Research Methods
Richa Bharti, Dominik G. Grimm
Summary: Analyzing the microbiome using next-generation sequencing techniques has improved our understanding of environmental microorganisms. However, analysis is affected by experimental conditions and downstream analysis, and new sequencing technologies can impact results. This work aims to review important workflows for sequencing data and provide best-practice protocols.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Engineering, Environmental
Qiaowen Tan, Weiying Li, Xiao Chen
Summary: This study investigated the importance of bacterial diversity in source tracking of fecal contamination, comparing the performances of different classification models. The results showed that the SVM model had the highest accuracy on local samples, indicating its efficiency and accuracy in fecal source tracking.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Immunology
Vitor Heidrich, Lilian T. Inoue, Paula F. Asprino, Fabiana Bettoni, Antonio C. H. Mariotti, Diogo A. Bastos, Denis L. F. Jardim, Marco A. Arap, Anamaria A. Camargo
Summary: Accessibility to next-generation sequencing (NGS) has enabled the profiling of microbial communities. Choosing the right 16S rRNA hypervariable region for sequencing is critical. This study evaluated the performance of different hypervariable regions in male urinary microbiota profiling and found that V1V2 region is more suitable.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Yan Gu, Jihua Wang, Weijun Cai, Guoliang Li, Yu Mei, Shaohai Yang
Summary: The study investigated the effects of different nitrogen fertilizer applications on soil bacterial diversity and community structure in a sugarcane cropping system. Excessive nitrogen application led to decreased pH, increased available nitrogen, and lower yields, while also reducing bacterial species richness. Optimum nitrogen treatment promoted beneficial microorganisms such as Actinobacteria, Nitrospira, and Bacillus, supporting a healthier ecosystem and sustainable crop production.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Geochemistry & Geophysics
B. G. Moravec, V Keifer, R. A. Root, A. M. White, Y. Wang, Y. Olshansky, J. McIntosh, J. Chorover
Summary: Weathering profiles are complex and vary from near surface highly transformed materials to less weathered parent materials at depth. The impact of material properties on mineral weathering rates is difficult to resolve from field data, especially when different depths of the profiles are reacted with aggressive meteoric waters. Experimental weathering of extracted cores in controlled laboratory conditions showed mineral transformation rates depend on mineral assemblage, texture, and legacy of hydrothermal alteration.
Article
Ecology
Yongjian Chen, Julia W. Neilson, Priyanka Kushwaha, Raina M. Maier, Albert Barberan
Summary: Through metagenomic analysis of copiotrophic and oligotrophic microbial communities in arid-hyperarid regions, it was found that vegetated soils harbor microbial communities with higher ecological traits and growth rates, while oligotrophic microbial communities in bare soils possess a higher proportion of genes with unknown functions.
Article
Soil Science
Atsushi Nakao, Shiori Uno, Junta Yanai, Hideo Kubotera, Ryoji Tanaka, Robert A. Root, Takashi Kosaki
Summary: This study investigated volcanic ash soils collected from four sites near the volcanic crater of Mt. Aso in Japan, revealing the significant impact of Asian dust on the radiocesium interception potential of soils, which aids in predicting the spatial distribution patterns of radiocesium in soils.
Article
Environmental Sciences
Dongmei Wang, Robert A. Root, Jon Chorover
Summary: Treatment of acid mine tailings leachate with pristine biochar can effectively remove arsenic and provide sustained pH buffering. The highly functionalized surface of biochar enables effective removal of trivalent arsenic from mine drainage.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Environmental Sciences
Linnea K. Honeker, Kelsey R. Graves, Malak M. Tfaily, Jordan E. Krechmer, Laura K. Meredith
Summary: The study suggests that undetected compounds in soil may have higher volatility compared to detected compounds, indicating potential oversight of VOCs in typical soil metabolomic analytical techniques. This could lead to missing links in metabolic pathways and emphasize the importance of considering biases in research design and interpretation, or incorporating direct online measurement methods to capture the role of VOCs in soil systems.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2021)
Article
Engineering, Environmental
Linnea K. Honeker, Gina A. Hildebrand, Jane D. Fudyma, L. Erik Daber, David Hoyt, Sarah E. Flowers, Juliana Gil-Loaiza, Angelika Kuebert, Ines Bamberger, Christopher R. Anderton, John Cliff, Sarah Leichty, Roya AminiTabrizi, Juergen Kreuzwieser, Lingling Shi, Xuejuan Bai, Dusan Velickovic, Michaela A. Dippold, S. Nemiah Ladd, Christiane Werner, Laura K. Meredith, Malak M. Tfaily
Summary: This study examined the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species. The results showed that drought had species-specific impacts on metabolic profiles and spatial distribution in different plants. The presence of microbial also influenced root metabolic pathways.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Environmental Sciences
Priyanka Kushwaha, Julia W. Neilson, Raina M. Maier, Alicja Babst-Kostecka
Summary: This study characterized the diversity and structure of rhizosphere-influenced and background soil microbial communities in different plant populations with contrasting zinc and cadmium hyperaccumulation traits. Results showed strong associations between zinc and cadmium hyperaccumulation variation and site type, location, microbial community properties, fungal richness and diversity in the rhizosphere, and soil bioavailability of cadmium and zinc.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Geochemistry & Geophysics
Corin M. Hammond, Robert A. Root, Raina M. Maier, Jon Chorover
Summary: Understanding the temporal effects of organic matter input and water influx on metal lability and translocation is crucial for evaluating the success of phytostabilization in metalliferous mine tailings. This study investigated metal lability trends for three years at a mine tailings site in central Arizona and found that pH played a key role in metal mobility. The addition of organic matter enhanced the mobilization of chromium and long-term monitoring is necessary to evaluate the efficacy of phytostabilization in controlling subsurface metal contaminants.
Article
Environmental Sciences
Arthur Moses, Jean E. T. McLain, Aminata Kilungo, Robert A. Root, Leif Abrell, Sanlyn Buxner, Flor Sandoval, Theresa Foley, Miriam Jones, Monica D. Ramirez-Andreotta
Summary: With the increasing need for water conservation, efforts to increase harvested rainwater in the American Southwest have been made to meet municipal needs. However, environmental pollution is also prevalent, raising concerns about the quality of harvested rainwater. To better understand the impact of socio-demographic factors on home characteristics, rainwater harvesting infrastructure, gardening practices, and perception of environmental pollution, a 145-question Home Description Survey was administered to 167 participants of Project Harvest. The study found significant associations between race/ethnicity and community and participant responses on various aspects, such as proximity to potential sources of pollution, roof and water harvesting device materials, capacity and age of harvesting devices, garden amendments, supplemental irrigation, and previous contaminant testing. Furthermore, the study revealed idiosyncratic differences in how underserved communities perceive environmental pollution and historical land uses. The collection of such data can inform tailored environmental monitoring efforts, reduce environmental hazard exposure, and design future studies to meet the needs of environmentally disadvantaged communities.
JOURNAL OF ENVIRONMENTAL STUDIES AND SCIENCES
(2022)
Article
Environmental Sciences
Erika E. Rios-Valenciana, Osmar Menezes, Xi-Zhi Niu, Jonathan Romero, Robert A. Root, Jon Chorover, Reyes Sierra-Alvarez, Jim A. Field
Summary: Nitroguanidine (NQ) is a new military explosive component and hazardous substance that can generate toxic products in the environment, requiring treatment. Iron-based reactive minerals show potential for NQ remediation, although more research is needed.
ENVIRONMENTAL POLLUTION
(2022)
Article
Chemistry, Analytical
Robert A. Root, Jon Chorover
Summary: This study investigated the release kinetics of toxic metals from mine tailings dust particles using in vitro bioassay and X-ray absorption spectroscopy. Arsenate within jarosite and sorbed to ferrihydrite, as well as lead from anglesite, were identified as the principal sources of contamination in the near surface tailings. The bioaccessible fractions of arsenic and lead were found to be higher in gastric fluid than lung fluid simulant, and the release of these elements showed a parabolic dissolution pattern for fine, highly-reactive particles followed by slower release from less soluble sources. The release of arsenic in lung fluid was mainly from arsenic-substituted jarosite, while in gastric fluid, arsenic complexed on ferrihydrite surfaces was preferentially released and subsequently repartitioned to jarosite-like coordination at extended exposures. Lead was primarily dissolved in phosphate rich lung fluid and subsequently repartitioned back to the solid phase as pyromorphite.
ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS
(2023)
Article
Soil Science
Lia Q. R. Ossanna, Karen Serrano, Lydia L. Jennings, Jesse Dillon, Raina M. Maier, Julia W. Neilson
Summary: The reclamation of disturbed lands through revegetation following mine closure is critical to the environmental sustainability of hard rock mining. This five-year temporal study aimed to identify indicators of primary soil development on mine waste rock (WR) and the comparative effects of plant lifeform on soil development. The study found that seeded WR had a temporal increase in microbial biomass compared to unseeded areas, and targeted grass and shrub root zones demonstrated significant increases in specific cellulose and lignin degrading and N-cycling phylotypes. Shrub establishment showed greater fertility outcomes, with more extensive chemical and biological fertility development observed in shrub root zones relative to grass.
APPLIED SOIL ECOLOGY
(2023)
Article
Soil Science
Ruiqi Liu, Shuqiong Kong, Yixian Shao, Dawei Cai, Bing Bai, Xiaguo Wei, Robert A. Root, Xubo Gao, Chengcheng Li, Jon Chorover
Summary: In this study, the release behaviors and solid-liquid interface reactions of arsenic-containing iron minerals in simulated gastrointestinal bio-fluids were investigated. The results showed that goethite released 0.57 mg/L and hematite released 0.82 mg/L of arsenic, with bioaccessibility of 10.8% and 21.6% respectively. The release of arsenic was mainly coupled with acid dissolution and reductive dissolution of iron minerals, and proteases enhanced its mobilization. Calcium chloride reduced the bioaccessibility of arsenic, suggesting that calcium-rich food or drugs may be effective in reducing arsenic toxicity.
Article
Agronomy
Yongjian Chen, David A. Dierig, Guangyao (Sam) Wang, Diaa Eldin M. Elshikha, Dennis T. Ray, Albert Barberan, Raina M. Maier, Julia W. Neilson
Summary: Plant-microbe associations and microbe-microbe associations are closely related, with critical microbes impacting the growth and health of plants. Through marker gene amplicon sequencing, the study identified overlapping critical microbes in both types of associations, highlighting their importance in the guayule agroecosystem.
Article
Microbiology
Cecilia Demergasso, Julia W. Neilson, Cinthya Tebes-Cayo, Roberto Veliz, Diego Ayma, Daniel Laubitz, Albert Barberan, Guillermo Chong-Diaz, Raina M. Maier
Summary: This study conducted a simulated rainfall experiment in the Atacama Desert and found that bacterial communities in extreme hyperarid soils have different responses to simulated rainfall and varied metabolic capacities due to historic exposure to aridity.
FRONTIERS IN MICROBIOLOGY
(2023)
