Editorial Material
Microbiology
Jimmy H. W. Saw
Summary: Microbial communities are often dominated by a few species, with a long tail of rare biosphere microorganisms that are highly diverse but found in low abundance. They play important roles in maintaining community integrity and resilience, and their phylogenetic diversity is crucial for understanding microbial diversity and evolution. Further efforts should be made to study these poorly understood microbial lineages that hold vast potential for advancing our understanding of microbial diversity, ecology, and evolution on Earth.
Article
Biochemistry & Molecular Biology
Yichen Hu, Amnon Amir, Xiaochang Huang, Yan Li, Shi Huang, Elaine Wolfe, Sophie Weiss, Rob Knight, Zhenjiang Zech Xu
Summary: This study tracked the dynamic changes of the saliva microbiome during human activities through a dense time series data. The results showed that eating activity significantly affected the salivary microbiota composition, with certain bacteria increasing after each meal. The composition of the microbiome also exhibited diurnal oscillation patterns at different taxonomy levels. This research emphasizes the importance of considering daily activities and diurnal factors in the design of oral microbiome studies.
Article
Multidisciplinary Sciences
William R. Shoemaker, Stuart E. Jones, Mario E. Muscarella, Megan G. Behringer, Brent K. Lehmkuhl, Jay T. Lennon
Summary: Research shows that under limited resources, most bacterial taxa can survive, with a wide range of extinction times. Despite the lack of exogenous resources, bacterial populations continue to evolve and acquire numerous mutations. While adapting to environmental pressures, bacterial lifespan is extended through scavenging dead cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Mireia Mestre, Juan Hofer
Summary: Despite the recent increase in knowledge about microorganisms, the processes determining their global distribution and functioning have not been fully understood. Microbial dormant stages are adapted to specific adverse conditions related to their dispersion path, indicating that dispersion is not completely random. Long-term dormancy enhances microbial dispersion, promoting their ubiquity. The global, recurrent, and spatially cyclical dispersion of microorganisms, known as the Microbial Conveyor Belt, directly influences microbial distribution and the functioning of the Earth system.
TRENDS IN MICROBIOLOGY
(2021)
Article
Ecology
Sana Romdhane, Ayme Spor, Julie Aubert, David Bru, Marie-Christine Breuil, Sara Hallin, Arnaud Mounier, Sarah Ouadah, Myrto Tsiknia, Laurent Philippot
Summary: This study utilized a top-down manipulation approach to investigate the role of biotic interactions in shaping soil microbial communities, revealing the importance of such interactions and identifying microbial community assembly rules. Modified biotic interactions had a greater impact on activities related to nitrogen cycling than carbon cycling, providing insights into microbial interactions in complex ecosystems and their relationship with ecosystem function.
Article
Biochemistry & Molecular Biology
Feilun Wu, Yuanchi Ha, Andrea Weiss, Meidi Wang, Jeffrey Letourneau, Shangying Wang, Nan Luo, Shuquan Huang, Charlotte T. Lee, Lawrence A. David, Lingchong You
Summary: Spatial partitioning modulates the dynamics of microbial communities, promoting the persistence of populations with negative interactions and suppressing those with positive interactions. An intermediate level of partitioning maximizes the overall diversity of the community.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Ecology
Lucie A. Malard, Antoine Guisan
Summary: The environmental niche concept can be used to understand the distribution of a taxon in the environment and its impact on community dynamics, biological invasions, and environmental changes. However, its application in microbial ecology is still limited due to the complexity of microbial systems and methodological limitations. The development of shot-gun metagenomics and metatranscriptomics provides new ways to investigate microbial niches and their metabolic activities within the environmental space.
TRENDS IN ECOLOGY & EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Ricardo Sousa, Joana Vasconcelos, Ivan Vera-Escalona, Joao Delgado, Mafalda Freitas, Jose A. Gonzalez, Rodrigo Riera
Summary: The study showed significant differences in observed OTUs among regions and identified three distinct groups based on presence/absence beta diversity analysis, with one group from the Azores, a second from Madeira, and a third from mainland Portugal, Selvagens, and the Canaries. These results are mainly driven by large-scale oceanographic processes in the study region, particularly the North Atlantic Subtropical Gyre and the Canary Current. The feasibility of using microbiome as a model study to understand biogeographic and evolutionary processes in marine species with high dispersal potential was suggested by the findings.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Usha F. Lingappa, Nathaniel T. Stein, Kyle S. Metcalfe, Theodore M. Present, Victoria J. Orphan, John P. Grotzinger, Andrew H. Knoll, Elizabeth J. Trower, Maya L. Gomes, Woodward W. Fischer
Summary: Climate change has led to extreme weather and rising sea levels, posing significant threats to coastal environments. Microbial mats, complex ecosystems, have been affected by sea level rise. Hurricane Irma in 2017 caused damage to an island in the Turks and Caicos Islands, but the microbial communities rapidly recovered and adapted to the changing sea level.
Article
Ecology
Davide Ciccarese, Gabriele Micali, Benedict Borer, Chujin Ruan, Dani Or, David R. Johnson
Summary: This study explores the growth and spatial self-organization of microbial co-cultures and reveals the emergence of rare and highly localized clusters, referred to as spatial jackpot events, that help stabilize the composition of the microbial community under fluctuating environmental conditions. A mechanistic agent-based mathematical model is used to understand the underlying mechanisms for the formation of these spatial jackpot events.
Article
Biochemistry & Molecular Biology
Caroline Vernette, Nicolas Henry, Julien Lecubin, Colomban de Vargas, Pascal Hingamp, Magali Lescot
Summary: The Ocean Barcode Atlas (OBA) is a user-friendly web service that allows biologists to explore the biodiversity and biogeography of marine organisms through DNA metabarcode data sets. Users can visualize a comprehensive picture of taxon diversity or barcode sequences on world maps and interactive charts, as well as adjust thresholds and view diversity results in the environmental context of sampling.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Environmental Sciences
Jennifer M. Polinski, Mattie Rodrigue, Jason D. Meyer, Matthew J. Harke
Summary: This study focuses on hydrothermal vent plume waters above the Moytirra hydrothermal vent field and examines the biodiversity and metabolic activities of the microbial communities in the plume. The results reveal a rich diversity of microorganisms and suggest the importance of sulfur compounds as an energy source in these waters. The study also highlights the decreasing metabolic functions and quiescent stages of bacterial communities with distance from the vent source.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Alma Dal Co, Martin Ackermann, Simon van Vliet
Summary: Most bacteria live in dense, spatially structured communities such as biofilms, where metabolic processes are spatially organized. This spatial organization is influenced by factors like cell mobility and local microenvironment. The arrangement of metabolic activities in space and the exchange of metabolites between cells in different regions play a crucial role in the overall metabolic activity and the ecology and evolution of microbial communities. This review discusses the mechanisms behind the spatial organization of metabolic processes in microbial systems and highlights key questions for future research.
Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Xavier Arnan, Elena Angulo, Raphael Boulay, Roberto Molowny-Horas, Xim Cerda, Javier Retana
Summary: This study aimed to examine the climatic niche similarity in native and introduced ant species in Europe, and found a strong phylogenetic signal in the optimal climatic niches of the most common ant species in Europe. Introduced species occupied different climatic niches in Europe compared to their native ranges, and their European climatic niches did not resemble those of their closest relative species in Europe.
SCIENTIFIC REPORTS
(2021)
Article
Agronomy
Juana Munoz-Ucros, Roland C. Wilhelm, Daniel H. Buckley, Taryn L. Bauerle
Summary: The study found that plants are affected by the legacy effects of drought on the rhizosphere microbiome. This drought legacy was propagated and persisted throughout nine weeks of plant growth, independent of prevailing water stress. Drought-impacted rhizospheres had larger populations of desiccation-tolerant and putatively endophytic taxa with established plant growth promoting capabilities.
Article
Soil Science
Roland C. Wilhelm, Harold M. van Es, Daniel H. Buckley
Summary: The study evaluated the accuracy of using microbiome data to predict soil health metrics, with biological health ratings better predicted than chemical or physical ratings. Models trained at the highest taxonomic resolution were the most accurate, with losses in accuracy resulting from rarefying, sparsity filtering, and aggregating at higher taxonomic ranks.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Soil Science
Roland C. Wilhelm, Laurel Lynch, Tara M. Webster, Steffen Schweizer, Thiago M. Inagaki, Malak M. Tfaily, Ravi Kukkadapu, Carmen Hoeschen, Daniel H. Buckley, Johannes Lehmann
Summary: The persistence of soil organic carbon (SOC) is influenced by soil properties, organic matter quality, and climatic conditions. This study compared the susceptibility of newly formed SOC to mineralization in soils developed under different precipitation regimes. The results showed that the susceptibility of SOC to mineralization was affected by iron content and mineralogy, initial SOC, substrate solubility, and microbial substrate use efficiency.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Microbiology
Janani Hariharan, Daniel H. Buckley
Summary: Dispersal is limited for most microbial taxa, and elevation gradients and habitat preferences play important roles in shaping the biogeography of Streptomyces bacteria.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Bhavya Sridhar, Gregory B. Lawrence, Spencer J. Debenport, Timothy J. Fahey, Daniel H. Buckley, Roland C. Wilhelm, Christine L. Goodale
Summary: Soil microbial community composition is closely related to pH, and liming can have immediate and long-lasting effects on the structure and function of bacterial and fungal communities in acid forest soils.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Samuel E. Barnett, Nicholas D. Youngblut, Daniel H. Buckley
Summary: Soil dwelling microorganisms play a crucial role in the carbon cycle by both degrading and stabilizing soil organic matter. However, the factors that drive the variation in bacterial community structure and function with respect to land use are still poorly understood. In this study, a multi-substrate DNA stable isotope probing experiment was conducted to examine the dynamics of bacterial growth and carbon assimilation in different land-use habitats. The results showed that carbon mineralization, community composition, and carbon assimilation dynamics all varied with land use. Furthermore, microbial community dynamics were found to influence carbon assimilation dynamics and were associated with soil DNA content. The findings suggest that soil DNA yield, which is easily measurable, may be a useful indicator for predicting microbial community dynamics related to soil carbon cycling.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biodiversity Conservation
Bhavya Sridhar, Roland C. Wilhelm, Spencer J. Debenport, Timothy J. Fahey, Daniel H. Buckley, Christine L. Goodale
Summary: Soil pH is closely related to microbial community structure and function, and this study demonstrates how pH can significantly impact carbon storage in forest soils by influencing the structure of bacterial and fungal communities that drive decomposition.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Elliot W. Jackson, Roland C. Wilhelm, Daniel H. Buckley, Ian Hewson
Summary: This study characterized the RNA virome of 38 echinoderm species from all five classes, revealing the diversity of RNA viruses in echinoderms. The study found that the relative viral representation did not significantly differ between different life stages, with the majority of viral contigs discovered from adult tissue transcriptomes.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Environmental Sciences
Roland C. Wilhelm, Juana Munoz-Ucros, Fabian Weikl, Karin Pritsch, Marc Goebel, Daniel H. Buckley, Taryn L. Bauerle
Summary: Mixed forest stands exhibit greater drought resistance compared to single-species stands due to complementarity in root ecology and physiology. This study investigates whether differences in the drought resistance of soil microbiomes contribute to this phenomenon. The results indicate that changes in soil moisture primarily affect bacteria, particularly Rhizobiales, while fungi, including ectomycorrhizal fungi, are generally unaffected. The resistance of the soil microbiome is higher in spruce root zones compared to beech root zones, corresponding to the proportions of drought-tolerant and drought-sensitive bacterial taxa. Mixed-species root zones contain a hybrid microbiome associated with both beech and spruce. The relative abundances of soil bacteria closely track moisture gradients and are more predictive of soil water content than other environmental variables.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Samuel E. Barnett, Rob Egan, Brian Foster, Emiley A. Eloe-Fadrosh, Daniel H. Buckley
Summary: Soil microbes play a crucial role in the global carbon cycle, but our understanding of how the carbon cycle operates in soil communities is limited. This is mainly due to the lack of functional genes that define carbon transformations. Through metagenomic stable isotope probing, we linked genomic features of bacteria to their carbon acquisition and growth dynamics in soil. We identified genomic traits that can predict bacterial ecological strategies, providing insights into bacterial interactions with soil carbon.
Article
Microbiology
Wyatt C. Tran, Brendan Sullivan, Claire E. Kitzmiller, Mallory Choudoir, Rachel Simoes, Nipuni Dayarathne, Kristen M. Deangelis
Summary: Paenibacillus sp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with a length of 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate belongs to a novel bacterial species.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Claire E. Kitzmiller, Wyatt C. Tran, Brendan Sullivan, Florencia Cortez, Mallory Choudoir, Rachel Simoes, Nipuni Dayarathne, Kristen M. Deangelis
Summary: This article reports the genome assembly and annotation of two Paenibacillus spp. strains (RC334 and RC343) isolated from a long-term soil warming experiment.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Brendan Sullivan, Claire E. Kitzmiller, Wyatt C. Tran, Mallory Choudoir, Rachel Simoes, Nipuni Dayarathne, Kristen M. DeAngelis
Summary: The complete genome sequence of Bacillus thuringiensis strain RC340, isolated from an environmental microbiology experiment soil sample, is presented. The genome of B. thuringiensis strain RC340 sequenced by GridION contains 5.86 million bases, 8,152 predicted genes, and 0.23% contamination.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Ecology
Roland C. Wilhelm, Joseph P. Amsili, Kirsten S. M. Kurtz, Harold M. van Es, Daniel H. Buckley
Summary: Soil microbiomes are influenced by soil conditions and can serve as 'bioindicators' for soil health assessment. However, limited information about most microorganisms hampers our ability to interpret the associations of bioindicators and their utility for management guidance.
ISME COMMUNICATIONS
(2023)
