Article
Microbiology
Cristina Casto-Rebollo, Maria Jose Argente, Maria Luz Garcia, Ramona Natacha Pena, Agustin Blasco, Noelia Ibanez-Escriche
Summary: This study reveals that selection for environmental variance (V-E) of litter size can alter the gut microbiome composition of rabbits, impacting immune regulation and resilience. The low V-E population showed suppressed abundance of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, and increased abundance of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, among others. These results highlight the connection between gut immune modulation and resilience.
Article
Environmental Sciences
Ya Zhang, Daliang Ning, Linwei Wu, Mengting Maggie Yuan, Xishu Zhou, Xue Guo, Yuanliang Hu, Siyang Jian, Zhifeng Yang, Shun Han, Jiajie Feng, Jialiang Kuang, Carolyn R. Cornell, Colin T. Bates, Yupeng Fan, Jonathan P. Michael, Yang Ouyang, Jiajing Guo, Zhipeng Gao, Zheng Shi, Naijia Xiao, Ying Fu, Aifen Zhou, Liyou Wu, Xueduan Liu, Yunfeng Yang, James M. Tiedje, Jizhong Zhou
Summary: The authors investigated the response of Archaea to experimental warming in a tallgrass prairie ecosystem and found that warming led to reduced diversity and convergent succession in the archaeal community. They also observed changes in ecosystem function. Although stochastic processes dominated community changes, their importance decreased over time. This study highlights the importance of understanding the temporal succession of ecological communities and the mechanisms underlying their responses to climate warming. The findings provide insights into the response of the Archaea domain to warming, which is still poorly understood.
NATURE CLIMATE CHANGE
(2023)
Article
Biotechnology & Applied Microbiology
Theresa Zwiener, Marina Dziuba, Frank Mickoleit, Christian Rueckert, Tobias Busche, Jorn Kalinowski, Rene Uebe, Dirk Schueler
Summary: The study established an approach for combinatory genome reduction in Magnetospirillum gryphiswaldense, resulting in a library of strains with multiple regions removed. A compact cassette comprising key magnetosome biosynthetic gene clusters replaced the fragmented genomic magnetosome island, showing wild type-like cell growth and magnetosome biosynthesis under optimal conditions, as well as improved resilience and genetic stability. This proof-of-principle for multiple genome reduction and large-scale engineering of magnetotactic bacteria will be valuable for synthetic biology and nanoparticle production.
MICROBIAL CELL FACTORIES
(2021)
Article
Environmental Sciences
Xuhui Zhang, Matthew C. Reid
Summary: This study reveals that methane generation activity can suppress the biovolatilization of arsenic in flooded rice paddy soil by enhancing the rate of arsenic demethylation. This finding contributes to a better understanding of the biogeochemical processes regulating arsenic biovolatilization in anaerobic soil environments.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Sofia Raffaelli, Eduardo Abreo, Nora Altier, Alvaro Vazquez, Silvana Albores
Summary: Antibiotic resistance is a growing concern in public health, and bacterial biofilms play an important role in recurrent or chronic infections. This study explored antimicrobial and antibiofilm extracts from soil bacteria and insect gut bacteria, and identified a potential candidate from Bacillus cereus ILBB55 for drug discovery to treat infectious diseases and inhibit biofilms of Staphylococcus aureus and Pseudomonas aeruginosa.
Article
Biochemistry & Molecular Biology
Fernando Puente-Sanchez, Matthias Hoetzinger, Moritz Buck, Stefan Bertilsson
Summary: Microorganisms exhibit high adaptability at the genome level, with heritable traits emerging in response to environmental niches. The pangenome concept, which partitions genomes into core and accessory regions, is valuable for studying microbial ecology and evolution. In this study, SuperPang, an algorithm that generates pangenome assemblies from input genomes, is presented. SuperPang provides a modular view of the pangenome, allowing the analysis of allelic and gene content variation. The algorithm is demonstrated through an analysis of intra-species diversity in the Polynucleobacter genus.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Plant Sciences
Maryam Foroozani, Matthew P. Vandal, Aaron P. Smith
Summary: The H3K4me3 histone mark in plants plays a crucial role in regulating gene expression and transcriptional memory, affecting various developmental processes and stress responses.
Article
Environmental Sciences
Tian Feng, Shuyu Zhao, Lang Liu, Xin Long, Chao Gao, Naicheng Wu
Summary: The study shows that soil bacteria in the North China Plain emit abundant HONO during the summer, with varying emission rates across different areas and clear diurnal cycles. HONO emissions from soil bacteria significantly affect atmospheric chemistry in the region, particularly in altering diurnal cycles of HONO and OH concentrations.
Review
Environmental Sciences
Gabrijel Ondrasek, Zed Rengel
Summary: Many of Earth's freshwater and land resources are affected by salinization, leading to destructive effects on ecosystems and agriculture. Traditional ameliorative strategies, along with advancements in biotechnology and ecoengineering, offer potential solutions to combat salinity, but knowledge gaps and ethical concerns remain to be addressed for successful industrial-scale implementation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Multidisciplinary Sciences
Stephan Koestlbacher, Astrid Collingro, Tamara Halter, Frederik Schulz, Sean P. Jungbluth, Matthias Horn
Summary: Researchers analyzed 82 metagenome-assembled genomes of Chlamydiae, identifying seven new families and describing genomic signals of metabolic diversity, which provides an extended perspective on the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Kai-Wei Yu, Peng Xue, Yang Fu, Liang Yang
Summary: The bacterial type VI secretion system (T6SS) is a protein secretion apparatus widely distributed in Gram-negative bacterial species, used for competition and coordination of invasion processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Hoon Je Seong, Jin Ju Kim, Taeyune Kim, Sung Jae Ahn, Mina Rho, Woo Jun Sul
Summary: This study conducted in-depth metagenome sequencing to investigate the distribution of environmental resistome and antibiotic-resistant bacteria (ARB) in shrimp farms, revealing a higher diversity of resistomes at early post-larval stages. Dominant presence of opportunistic pathogens with virulence factors like Francisella, Mycoplasma, Photobacterium, and Vibrio in shrimp farms highlights the increased resistance diversity and environmental selection of pathogens.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Environmental Sciences
Yu-Pin Lin, Rainer Ferdinand Wunderlich, Chiao-Ming Lin, Norman Uphoff, Dirk S. Schmeller, Oleg Shipin, Teiji Watanabe, Ngadisih, Hussnain Mukhtar
Summary: The study found that the diversity of archaea and bacteria in soil is influenced by land cover types and environmental zones, with archaeal beta-diversity mainly controlled by environmental zones. These results highlight the importance of land cover types and environmental zones for understanding the contributions of soil microbes to nutrient dynamics and ecosystem resilience.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Microbiology
Samuel C. Forster, Simon Clare, Benjamin S. Beresford-Jones, Katherine Harcourt, George Notley, Mark D. Stares, Nitin Kumar, Amelia T. Soderholm, Anne Adoum, Hannah Wong, Belen Moron, Cordelia Brandt, Gordon Dougan, David J. Adams, Kevin J. Maloy, Virginia A. Pedicord, Trevor D. Lawley
Summary: A study on a mouse model of inflammatory bowel disease reveals that the gut microbiome plays a crucial role in the variability across genetically identical mice, and identifies two bacterial species that affect treatment outcomes differently. This finding is important for the improvement of mouse models for human intestinal diseases.
NATURE MICROBIOLOGY
(2022)
Article
Biology
Jin-Long Yang, Dan-Dan Feng, Jie Liu, Jia-Kang Xu, Ke Chen, Yi-Feng Li, You-Ting Zhu, Xiao Liang, Ying Lu
Summary: The study constructed a chromosome-level genome of the hard-shelled mussel using advanced sequencing technologies, revealing high genome completeness and facilitating gene annotation. Phylogenetic analysis showed the evolutionary relationship of M. coruscus with other bivalves, and transcriptomic profiling identified signaling pathways involved in metamorphosis.
Article
Multidisciplinary Sciences
Eric W. Seabloom, Elizabeth T. Borer, Yvonne M. Buckley, Elsa E. Cleland, Kendi F. Davies, Jennifer Firn, W. Stanley Harpole, Yann Hautier, Eric M. Lind, Andrew S. MacDougall, John L. Orrock, Suzanne M. Prober, Peter B. Adler, T. Michael Anderson, Jonathan D. Bakker, Lori A. Biederman, Dana M. Blumenthal, Cynthia S. Brown, Lars A. Brudvig, Marc Cadotte, Chengjin Chu, Kathryn L. Cottingham, Michael J. Crawley, Ellen I. Damschen, Carla M. Dantonio, Nicole M. DeCrappeo, Guozhen Du, Philip A. Fay, Paul Frater, Daniel S. Gruner, Nicole Hagenah, Andy Hector, Helmut Hillebrand, Kirsten S. Hofmockel, Hope C. Humphries, Virginia L. Jin, Adam Kay, Kevin P. Kirkman, Julia A. Klein, Johannes M. H. Knops, Kimberly J. La Pierre, Laura Ladwig, John G. Lambrinos, Qi Li, Wei Li, Robin Marushia, Rebecca L. McCulley, Brett A. Melbourne, Charles E. Mitchell, Joslin L. Moore, John Morgan, Brent Mortensen, Lydia R. O'Halloran, David A. Pyke, Anita C. Risch, Mahesh Sankaran, Martin Schuetz, Anna Simonsen, Melinda D. Smith, Carly J. Stevens, Lauren Sullivan, Elizabeth Wolkovich, Peter D. Wragg, Justin Wright, Louie Yang
NATURE COMMUNICATIONS
(2015)
Article
Environmental Sciences
Elliott G. Duncan, Cathryn A. O'Sullivan, Anna K. Simonsen, Margaret M. Roper, Karen Treble, Kelley Whisson
Article
Multidisciplinary Sciences
Anna K. Simonsen, Russell Dinnage, Luke G. Barrett, Suzanne M. Prober, Peter H. Thrall
NATURE COMMUNICATIONS
(2017)
Article
Soil Science
Elliott G. Duncan, Cathryn A. O'Sullivan, Anna K. Simonsen, Margaret M. Roper, Mark B. Peoples, Karen Treble, Kelley Whisson
Article
Biology
Tia L. Harrison, Anna K. Simonsen, John R. Stinchcombe, Megan E. Frederickson
Article
Plant Sciences
Russell Dinnage, Anna K. Simonsen, Luke G. Barrett, Marcel Cardillo, Nat Raisbeck-Brown, Peter H. Thrall, Suzanne M. Prober
JOURNAL OF ECOLOGY
(2019)
Article
Ecology
Anna K. Simonsen, Luke G. Barrett, Peter H. Thrall, Suzanne M. Prober
Article
Plant Sciences
Rebecca T. Batstone, Madeline A. E. Peters, Anna K. Simonsen, John R. Stinchcombe, Megan E. Frederickson
AMERICAN JOURNAL OF BOTANY
(2020)
Article
Biology
Julia A. Boyle, Anna K. Simonsen, Megan E. Frederickson, John R. Stinchcombe
Summary: Priority effects occur when the order of species arrival affects the final community structure. In the case of mutualists interacting with hosts in different orders, the outcome can be influenced by the interaction order, with hosts receiving high-quality mutualists early better tolerating low-quality symbionts later.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Pedro M. Tognetti, Suzanne M. Prober, Selene Baez, Enrique J. Chaneton, Jennifer Firn, Anita C. Risch, Martin Schuetz, Anna K. Simonsen, Laura Yahdjian, Elizabeth T. Borer, Eric W. Seabloom, Carlos Alberto Arnillas, Jonathan D. Bakker, Cynthia S. Brown, Marc W. Cadotte, Maria C. Caldeira, Pedro Daleo, John M. Dwyer, Philip A. Fay, Laureano A. Gherardi, Nicole Hagenah, Yann Hautier, Kimberly J. Komatsu, Rebecca L. McCulley, Jodi N. Price, Rachel J. Standish, Carly J. Stevens, Peter D. Wragg, Mahesh Sankaran
Summary: Nitrogen addition decreases the abundance and diversity of legumes in grasslands, especially in nitrogen-poor soils, while increasing the cover of non-nitrogen fixing plants. The addition of phosphorus, potassium, and other nutrients can enhance the abundance of legumes, but does not counteract the negative effects of nitrogen addition.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Zoe. A. A. Parshuram, Tia. L. L. Harrison, Anna. K. K. Simonsen, John. R. R. Stinchcombe, Megan. E. E. Frederickson
Summary: Both mutualism and polyploidy can influence plant invasion success, but their joint effects have been rarely studied. This study showed that polyploid legume species have been successfully introduced to new ranges, but their range expansion is constrained by interactions with rhizobia. In contrast, diploid legume species have limited spread regardless of symbiotic status with rhizobia.
Article
Biology
Pooja Nathan, Evan P. Economo, Benoit Guenard, Anna K. Simonsen, Megan E. Frederickson
Summary: Mutualism plays an important role in the spread and adaptation of species in new environments. Generalized mutualisms increase the likelihood of species establishing and thriving beyond native ranges, while specialized mutualisms do not affect or even reduce non-native spread.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Plant Sciences
Samuel C. Andrew, Pieter A. Arnold, Anna K. Simonsen, Veronica F. Briceno
Summary: This study investigated the heat tolerance of Acacia species in response to heatwaves and found that they displayed significant heat acclimation responses, which may explain their diversity and ubiquity in arid Australian ecosystems.
FUNCTIONAL PLANT BIOLOGY
(2023)
Article
Microbiology
Ming-Dao Chia, Anna K. Simonsen
Summary: In this study, complete genome sequences of four Bradyrhizobium sp. strains isolated from the root nodules of Acacia acuminata were reported using a hybrid long- and short-read assembly approach. The genome sizes ranged between 7.1Mbp and 8.1Mbp, each containing a single circular chromosome. Whole-genome alignments revealed extensive structural rearrangement.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)