Article
Fisheries
Socorro Toxqui-Rodriguez, Fernando Naya-Catala, Ariadna Sitja-Bobadilla, M. Carla Piazzon, Jaume Perez-Sanchez
Summary: This study compared different sequencing platforms for microbial characterization in fish gut mucosal samples. The results showed that MinION is a reliable and accurate tool for assessing intestinal bacteria communities, with good correlation with Illumina results. However, less abundant but biologically important taxa may be masked compared to Illumina sequencing.
Article
Environmental Sciences
Adithya Govindarajan, Mary Crum, Jay Adolacion, Amin Kiaghadi, Edgar Acuna-Gonzalez, Hanadi S. Rifai, Richard C. Willson
Summary: This study provides a description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey. The presence and abundance of specific bacterial and archaeal taxa indicate pollutant inputs and the study also observed microorganisms involved in the biodegradation of xenobiotics. The spatial occurrence of a specific degrader of persistent polychlorinated compounds is explained by sediment properties and contaminant concentrations.
MARINE POLLUTION BULLETIN
(2022)
Article
Biotechnology & Applied Microbiology
Xianya Zou, Yukiko Nakura, Haruna Kawaguchi, Fumiko Nishiumi, Heng Ning Wu, Itaru Yanagihara
Summary: This study aimed to compare the effectiveness of different databases in comprehensively identifying potentially pathogenic vaginal microbiota in Japanese women through bioinformatic analysis, and the results showed that the BLAST database was the best choice for NGS data analysis of Japanese women's vaginal microbiota.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Immunology
Birgit Fritz, Edita Paschko, Wayne Young, Daniel Boehringer, Siegfried Wahl, Focke Ziemssen, Markus Egert
Summary: Slit lamps are commonly used for examining numerous patients and are often contaminated with bacteria from human skin, mucosa, and possibly eyes. The study showed a diverse bacterial microbiota on slit lamps, emphasizing the importance of thorough cleaning and disinfection to prevent infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
Yu-Kun Zhang, Qian Zhang, Yu-Liuming Wang, Wei-Yuan Zhang, Han-Qing Hu, Hong-Yu Wu, Xiang-Zong Sheng, Kang-Jia Luo, Hao Zhang, Meng Wang, Rui Huang, Gui-Yu Wang
Summary: This study revealed differences in intestinal microbiota composition among groups of CRC patients, young volunteers, and old volunteers. The enrichment of specific bacteria in different age groups and in CRC patients suggests potential protective or tumorigenic roles, highlighting the importance of gut bacteria in colorectal cancer.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Fisheries
Yufeng Si, Jinxuan Wen, Yao Xu, Patarida Roengjit, Hao Wang
Summary: The 16S rRNA high throughput sequencing technology is increasingly used to discover pathogenic bacteria, with Edwardsiella identified as the main causative pathogen in the diseased turbot outbreak in China. This cost-effective and rapid technology helps in accurate pathogen identification and disease research.
AQUACULTURE REPORTS
(2021)
Article
Ecology
Xiaoai Cao, Huamin Liu, Yang Liu, Jin Jing, Lu Wen, Zhichao Xu, Xuhua Liu, Dongwei Liu, Yi Zhuo, Lixin Wang
Summary: Soil freeze-thaw processes in the wetlands of the Inner Mongolia Plateau lead to high N2O emissions and greenhouse effect exacerbation. This study investigated the effects of freeze, freeze-thaw, and thaw periods on bacterial community diversity and composition, as well as greenhouse gas emissions during spring thaw. The results showed that the freeze-thaw periods primarily impacted the diversity and composition of bacterial communities and revealed potential microbial mechanisms of N2O emission during spring thaw.
ECOLOGY AND EVOLUTION
(2023)
Article
Agronomy
Ko-Hsuan Chen, Reid Longley, Gregory Bonito, Hui-Ling Liao
Summary: The improved two-step PCR approach significantly enhances sequence quantity and recovery rate, while maintaining high read quality. By incorporating synthetic barcodes independently, this method can be broadly adapted to different genomic regions and organisms of scientific interest.
Article
Agronomy
Cassia Oliveira, Ehsan Shakiba, Dustin North, Madison McGraw, Ethan Ballard, Marissa Barrett-D'Amico, Galina Glazko, Yasir Rahmatallah
Summary: The rhizomicrobiome, composed of microbes living in association with plant roots, plays a crucial role in plant growth and crop yield. This study investigated the impact of crop rotation and soil cultivation methods on the diversity and composition of rhizosphere bacteria using metagenomic analysis. The results showed that crop rotation and tillage did not significantly affect bacterial diversity.
Article
Microbiology
Salma Mukhtar, Samina Mehnaz, Kauser Abdulla Malik
Summary: The study evaluated the microbial diversity of the rhizosphere and root endosphere of desert halophytes in arid environments of Pakistan, finding that Proteobacteria were more abundant in rhizospheric soils, while Actinobacteria were dominant in the root endosphere of halophytes. Bacillus, Kocuria, Pseudomonas, Halomonas, and Flavobacterium were commonly identified from the rhizosphere and root endosphere of halophytes across all three sites. This study highlights the potential for microbial diversity analysis to study the impact of abiotic factors on microbial communities associated with halophyte roots in arid regions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Wilbert Gutierrez-Sarmiento, Betsy Anaid Pena-Ocana, Anayancy Lam-Gutierrez, Jorge Martin Guzman-Albores, Ricardo Jasso-Chavez, Victor Manuel Ruiz-Valdiviezo
Summary: This study analyzed the physicochemical characteristics, microbial communities, and predictive metabolic functionalities of Tepache, a native beverage from Mexico. The research revealed significant changes in the physicochemical properties and microbial communities during the fermentation process. These findings contribute to the understanding of Tepache manufacturing and its potential health benefits.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Microbiology
Giuliano Netto Flores Cruz, Ana Paula Christoff, Luiz Felipe Valter de Oliveira
Summary: High-throughput sequencing of 16S rRNA amplicon is widely used for microbiome characterization globally, allowing direct analysis of sample bacterial composition. By recovering proportionality between observed read counts and absolute bacterial abundances, accurate estimation of bacterial numbers is possible. However, predictive performance of the model is affected by specific rare taxa.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Endocrinology & Metabolism
Qing Wang, Qi Wang, Lanbo Zhao, Yadi Bin, Li Wang, Lei Wang, Kailu Zhang, Qiling Li
Summary: The blood microbiome of PCOS patients showed significantly lower alpha diversity, different beta diversity, and significant taxonomic variations compared to healthy controls.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Microbiology
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing Lam, Alan Ka-Lun Wu, Gilman Kit-Hang Siu
Summary: In this study, two 16S rRNA gene sequencing tests based on the Illumina and Nanopore sequencing technologies were compared to identify clinical isolates that cannot be identified by MALDI-TOF MS. The results showed that the Nanopore workflow had a higher taxonomic resolution at the species level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dominika Salamon, Barbara Zapala, Agnieszka Krawczyk, Agnieszka Potasiewicz, Agnieszka Nikiforuk, Anastazja Stoj, Tomasz Gosiewski
Summary: This study compared the accuracy and efficacy of two Illumina platforms (iSeq and MiSeq) in sequencing 16S rRNA and described some important similarities and differences in 20 fecal samples. The results showed that iSeq technology had lower species richness compared to MiSeq, and MiSeq had a higher number of taxa. Additionally, MiSeq performed better in the detailed analysis of microbiota composition.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Grace Pold, Andrew F. Billings, Jeff L. Blanchard, Daniel B. Burkhardt, Serita D. Frey, Jerry M. Melillo, Julia Schnabel, Linda T. A. van Diepen, Kristen M. DeAngelis
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2016)
Article
Microbiology
Kelly Nicole Haas, Jeffrey L. Blanchard
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2017)
Article
Multidisciplinary Sciences
Frederik Schulz, Lauren Alteio, Danielle Goudeau, Elizabeth M. Ryan, Feiqiao B. Yu, Rex R. Malmstrom, Jeffrey Blanchard, Tanja Woyke
NATURE COMMUNICATIONS
(2018)
Article
Agronomy
Emily J. Cole, Omid R. Zandvakili, Baoshan Xing, Masoud Hashemi, Allen V. Barker, Steven J. Herbert
COMMUNICATIONS IN SOIL SCIENCE AND PLANT ANALYSIS
(2019)
Article
Microbiology
Kelly N. Haas, Jeffrey L. Blanchard
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2020)
Article
Microbiology
L. Alteio, F. Schulz, R. Seshadri, N. Varghese, W. Rodriguez-Reillo, E. Ryan, D. Goudeau, S. A. Eichorst, R. R. Malmstrom, R. M. Bowers, L. A. Katz, J. L. Blanchard, T. Woyke
Article
Microbiology
Jason P. Andras, William G. Rodriguez-Reillo, Alexander Truchon, Jeffery L. Blanchard, Erin A. Pierce, Katherine A. Ballantine
FEMS MICROBIOLOGY ECOLOGY
(2020)
Article
Engineering, Environmental
Rachelle E. LaCroix, Nicolas Walpen, Michael Sander, Malak M. Tfaily, Jeffrey L. Blanchard, Marco Keiluweit
Summary: Global warming accelerates microbial decomposition of soil organic matter, leading to a decrease in the redox capacity of water-extractable organic matter in soil. This decline may negatively impact critical biogeochemical processes such as microbial respiration, nutrient cycling, and contaminant degradation.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2021)
Correction
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I- Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
NATURE BIOTECHNOLOGY
(2021)
Article
Ecology
Gregory J. Pec, Linda T. A. van Diepen, Melissa Knorr, A. Stuart Grandy, Jerry M. Melillo, Kristen M. DeAngelis, Jeffrey L. Blanchard, Serita D. Frey
Summary: A study conducted at Harvard Forest found that long-term soil warming led to compositional shifts in soil fungal communities, particularly in the saprotrophic and unknown components, while short-term warming did not have a significant impact. Soil warming resulted in declines in soil C concentrations and total C stored in the organic horizon. Furthermore, after long-term warming, changes in fungal guild relative abundances were associated with substantial alterations in soil organic matter chemistry, particularly the abundance of lignin.
Article
Microbiology
Priyanka Roy Chowdhury, Stefan M. Golas, Lauren Alteio, Joshua T. E. Stevens, Andrew F. Billings, Jeffrey L. Blanchard, Jerry M. Melillo, Kristen M. DeAngelis
Summary: The study indicates that long-term climate warming has a significant impact on microbial degradation of carbon in the soil, potentially accelerating the carbon cycle in heated plots. Furthermore, it was found that heating leads to increased expression of specific enzymes in soil, particularly those related to carbohydrate and lipid metabolism.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Emily J. Cole, Omid R. Zandvakili, Baoshan Xing, Masoud Hashemi, Stephen Herbert, Hamid H. Mashayekhi
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)