Review
Ecology
Xueni Bian, Beulah H. Garner, Huaxi Liu, Alfried P. Vogler
Summary: Most insect communities are composed of diverse lineages, but there is a lack of detailed phylogenetic analysis of whole communities, especially in species-rich tropical ecosystems. The SITE-100 program aims to construct the Tree-of-Life by sampling high-biodiversity sites globally. The study uses large-scale high-resolution cameras for specimen imaging, DNA extraction, sequencing, and phylogenetic analysis. To overcome limitations and challenges, the research combines nuclear shotgun data, site-based mitochondrial genomes, and DNA barcodes in a hierarchical approach.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Carol Kim, Lorie W. Staver, Xuan Chen, Ashley Bulseco, Jeffrey C. Cornwell, Sairah Y. Malkin
Summary: We investigated the succession of soil microbial communities in newly constructed salt marshes using 16S rRNA amplicon sequences. The alpha diversity of subsurface horizons recovered to reference levels within 3 years, while alpha diversity in surface soils remained unchanged. Microbial community succession was faster in surface soils and slower in subsurface horizons. We found important taxa driving the trajectories towards reference conditions and observed co-development of sulfide and methane removal metabolisms in marsh soils.
Article
Biochemistry & Molecular Biology
Guangliang Zhang, Junhong Bai, Christoph C. Tebbe, Laibin Huang, Jia Jia, Wei Wang, Xin Wang, Lu Yu, Qingqing Zhao
Summary: This study investigates the effects of plant invasions on soil microbial communities and functions in salt marshes. It finds that microbial diversity is positively correlated with the duration of invasion, and both bacterial and fungal communities show consistent changes with invasion. The metabolic potential of soil microbes decreases in response to invasion, leading to carbon accumulation in invaded salt marshes. Bacteria and fungi have distinct contributions to microbial community assembly along the invasion gradient.
Article
Microbiology
Yanfen Zheng, Zongchang Xu, Haodong Liu, Yan Liu, Yanan Zhou, Chen Meng, Siqi Ma, Zhihong Xie, Yiqiang Li, Cheng-Sheng Zhang
Summary: This study investigates the microbiome and function signatures of salt-tolerant plants, revealing differences in bacterial communities and the importance of microbial function in enhancing plant adaptability to saline soil. Soil pH, electrical conductivity, and total nitrogen were identified as important driving factors for microbial and functional gene selection. Root exudates were suggested as a factor in the selection of rhizosphere and endosphere microbiota.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Bo Wang, Xicheng Wang, Zhuangwei Wang, Kefeng Zhu, Weimin Wu
Summary: This study explored the changes in the rhizosphere microbial community of salt-tolerant and salt-sensitive grapevines under salt stress using metagenomic sequencing. The results showed that salt stress had a greater impact on the rhizosphere microbiota of the salt-tolerant variety, with differentially enriched functions related to cell motility and metabolism. The composition and functions of the rhizosphere microbial community were found to contribute to the enhanced salt tolerance of certain grapevines.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Ecology
Katie Peterson, Megan Ruffley, Christine E. Parent
Summary: The study evaluated the effects of fragmentation on community assembly in Craters of the Moon National Monument and Preserve. Through traditional metrics and machine-learning models, it was found that neutral and filtering processes influenced the formation of plant communities in the fragmented system. Different kipukas exhibited varying ecological characteristics, with model support for competition decreasing as species richness increased and habitat filtering being more prominent in lower elevation kipukas.
ECOLOGY AND EVOLUTION
(2021)
Article
Environmental Sciences
Jakub Lach, Klaudyna Krolikowska, Monika Baranowska, Magdalena Krupinska, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Pawel Staczek
Summary: The Bochnia Salt Mine, established in the thirteenth century, is one of the oldest mines in Europe and was active until 1990. It has been recognized as a UNESCO World Heritage site. Previous research on Polish salt mines has mainly focused on bioaerosol characteristics, microorganism identification, and their potential health benefits. However, the biodiversity of salt mines and their biotechnological potential remain poorly characterized. This study examines the microbial biodiversity of the Bochnia Salt Mine and identifies potential biotechnological and pharmaceutical applications.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Microbiology
Paula Vidal, Monica Martinez-Martinez, Laura Fernandez-Lopez, Sergi Roda, Celia Mendez-Garcia, Olga V. Golyshina, Victor Guallar, Ana I. Pelaez, Manuel Ferrer
Summary: This study identifies enzymes with potential biotechnological interest from the Los Rueldos acid mine drainage (AMD) system. The enzymes, derived from acidophilic bacteria, exhibit high diversity and potential novelty. Some of these enzymes are adapted to acidic conditions and may have potential applications in plastic degradation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Alejandro Miguel Cisneros-Martinez, Luis E. Eguiarte, Valeria Souza
Summary: In spring 2016, a shallow hypersaline pond known as Archaean Domes (AD) was discovered in Cuatro Cienegas Basin (CCB). AD has a highly diverse microbial community and a unique viral community structure that remains stable regardless of environmental fluctuations. The diversity of AD is closely related to other CCB sites but forms a cluster of its own.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Paula Maza-Marquez, Michael D. Lee, Brad M. Bebout
Summary: The study evaluated the abundance and diversity of fungi in a hypersaline microbial mat from Guerrero Negro, Mexico, using qPCR and metagenomic sequencing. The findings revealed a rich fungal community structure with functions including saprotrophic, parasitic, and denitrification activities.
Article
Microbiology
Siew Herng Chan, Muhammad Hafiz Ismail, Chuan Hao Tan, Scott A. Rice, Diane McDougald
Summary: The study found that predation by protozoa and bacteriophage positively correlated with the formation of aerobic granules. The increase in abundance of filamentous phages may promote the structural formation of granules, while the absence of protozoa after chemical treatment delayed the initiation of granules formation.
Review
Genetics & Heredity
Nahui Olin Medina-Chavez, Michael Travisano
Summary: Archaea are a unique system for investigating the diversity of life, with the longest evolutionary history and the most diverse group of organisms. They exist in various environments, providing insight into the basis of survival under extreme conditions. Archaea are frequently found in microbial communities and have played a central role in the evolution of Eukaryotes. They can also be used as a proxy for studying life on other planets. Future advances will require both phylogenomic studies and improved techniques for isolation and cultivation.
FRONTIERS IN GENETICS
(2022)
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
Oceanography
Gu Chen, Shi Jiyan, Rui Jianliang, Yu Yamning, Huang Weibin, Lu Zhinai, Chen Yao, Chen Xiaojun, Dong Shudi, Hu Zhijun, Ye Chenghua
Summary: This study investigated the microbial community of salt marsh vegetation and associated soil in the coastal wetlands of Zhoushan Islands in China. Results showed that different wetland types had varying soil physio-chemical properties and microbial composition. This study provides important insights for understanding wetland microbial communities and ecosystem restoration.
JOURNAL OF OCEAN UNIVERSITY OF CHINA
(2022)
Article
Multidisciplinary Sciences
Hyunmin Koo, Casey D. Morrow
Summary: This study developed an analytic method to detect indicators of microbial strain dysbiosis and found shared gut commensal microbes in both healthy individuals and COVID-19 patients, suggesting a potential dysbiosis in the microbial strain community.
SCIENTIFIC REPORTS
(2022)
Review
Microbiology
David C. Karasz, Anna I. Weaver, Daniel H. Buckley, Roland C. Wilhelm
Summary: Bacteria can regulate cell morphology in response to environmental conditions, adopting a filamentous growth habit to optimize their growth and metabolism in highly variable environments. This trait can impact succession, symbioses, and biogeochemistry in soil environments.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Janani Hariharan, Mallory J. Choudoir, Peter Diebold, Kevin Panke-Buisse, Daniel H. Buckley
Summary: A novel Streptomyces strain, named Streptomyces apricus sp. nov., was isolated from soils in Wisconsin, USA. Genome sequencing revealed that this strain had low similarity to type species of Streptomyces. The results of a polyphasic study confirmed the novelty of this isolate.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
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
Microbiology
Ying Wang, Roland C. Wilhelm, Tami L. Swenson, Anita Silver, Peter F. Andeer, Amber Golini, Suzanne M. Kosina, Benjamin P. Bowen, Daniel H. Buckley, Trent R. Northen
Summary: Microorganisms' life-history strategies have a significant impact on the processing of organic carbon, which in turn influences microbial interactions and carbon cycling in soils. High rrn isolates have a greater potential for resource competition and tend to consume a wider variety and larger quantity of substrates compared to low rrn isolates. By connecting bacterial life-history strategies, genomic traits, and metabolism, this study advances our understanding of the links between bacterial community composition and the transformation of carbon in soils.
FRONTIERS IN MICROBIOLOGY
(2022)
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
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)