Article
Microbiology
Cody S. Sheik, Jonathan P. Badalamenti, Jon Telling, David Hsu, Scott C. Alexander, Daniel R. Bond, Jeffrey A. Gralnick, Barbara Sherwood Lollar, Brandy M. Toner
Summary: Deep subsurface environments host diverse microbial communities facing unique challenges, with nutrient limitations likely facilitating diverse microbe-microbe interactions that drive biogeochemical cycling of major elements. Microbial communities in low temperature, chemically reduced brines at the Soudan Underground Mine State Park are dominated by Firmicute and Proteobacteria phyla, with metabolic reconstruction showing dominant carbon-fixation pathways and potential for cryptic sulfur cycling. Overall, metabolic flexibility is an important trait for microorganisms in deep isolated systems.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Jesper N. Tegner
Summary: Machine translation now enables automatic detection of different cell types from single-cell transcriptomic data, allowing for the potential to dissect complex clinical samples like heterogeneous tumors at a large scale.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biotechnology & Applied Microbiology
Emily A. Kraus, Daniel Nothaft, Blake W. Stamps, Kaitlin R. Rempfert, Eric T. Ellison, Juerg M. Matter, Alexis S. Templeton, Eric S. Boyd, John R. Spear
Summary: The study explores the functional capability and activity of microbial methane cycling in serpentinization-impacted subsurface waters in the Samail Ophiolite of Oman. The results reveal active methanogenic and methanotrophic populations, particularly in waters with hyperalkaline pH. This highlights the potential for biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang
Summary: Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation and disease occurrence and progression. HUSCH is a large-scale database that integrates high-quality single-cell transcriptomic datasets from different tissues, providing comprehensive visualization and analysis of gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Environmental Sciences
Chong Xu, Shiquan Sun, Yifu Li, Yang Gao, Wei Zhang, Liu Tian, Tian Li, Qing Du, Jingju Cai, Lean Zhou
Summary: Sediment is a major source of water pollution, and its remediation is crucial for water purification. Sediment microbial fuel cells (SMFCs) have gained attention for their ability to remove organic pollutants, compete with methanogens, and recover energy. This paper provides a comprehensive review on the recent advances of SMFCs in sediment remediation, including the advantages and disadvantages of current technologies, the principles and influencing factors of SMFCs, their applications in pollutant removal and remote monitoring, and strategies for enhancing their performance in sediment bioremediation. The drawbacks of SMFCs and future development directions are also discussed.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemical Research Methods
Mengqi Zhang, F. Richard Guo
Summary: Single-cell sequencing has revolutionized the identification of differentially expressed genes (DEGs) by providing high resolution for heterogeneous cell tissues. However, current analysis mainly focuses on comparing different cell types within the same individual. This study proposes a nonparametric method called barycenter single-cell differential expression (BSDE) to identify DEGs in case-control studies. The method overcomes the limitations of parametric approaches and accurately detects differential expressions. It is demonstrated through simulations and real data analysis that BSDE can effectively identify cell type-specific DEGs. The availability of the R package and datasets further facilitate its application in research.
Article
Biochemistry & Molecular Biology
Dongqing Sun, Jin Wang, Ya Han, Xin Dong, Jun Ge, Rongbin Zheng, Xiaoying Shi, Binbin Wang, Ziyi Li, Pengfei Ren, Liangdong Sun, Yilv Yan, Peng Zhang, Fan Zhang, Taiwen Li, Chenfei Wang
Summary: Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade has shown significant efficacy, but only a minority of patients respond due to tumor microenvironment heterogeneity. TISCH is a large curated database that integrates single-cell transcriptomic profiles from 76 high-quality tumor datasets across 27 cancer types, providing a user-friendly interface for exploring gene expression atlas in the TME from multiple cancer types.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biotechnology & Applied Microbiology
Boxun Li, Gary C. Hon
Summary: As we approach a comprehensive catalog of mammalian cell types, the ability to engineer specific cell types on demand would revolutionize biomedical research and regenerative medicine. Direct reprogramming of cells through specific transcription factor cocktails offers a promising strategy for cell fate engineering. Recent advancements in single-cell technologies have overcome challenges in bulk reprogramming methods, accelerating progress in the field of cellular engineering.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Microbiology
Javier Vicente, Miguel de Celis, Alejandro Alonso, Domingo Marquina, Antonio Santos
Summary: Deception Island in Antarctica is a geothermal location with active fumaroles, creating a unique habitat for microbial communities. A multidisciplinary study on sediments deposited over 4 years revealed a bacterial community dominated by Proteobacteria and Thaumarchaeota, a fungal community mainly composed of Aspergillaceae, and the presence of diatoms. The study highlighted the significant influence of physicochemical conditions on microbial populations and their distribution, providing valuable data on the interaction between the island and water microbiota.
Review
Biochemical Research Methods
Mattia Forcato, Oriana Romano, Silvio Bicciato
Summary: Recent advances in single-cell technologies are providing exciting opportunities for dissecting tissue heterogeneity and investigating cell identity, fate and function. However, combining different single-cell genomic signals is computationally challenging and requires integrative analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Environmental Sciences
Yun Ma, Tianwei Xu, Qiao Mao, Xinmei Zhou, Rui Wang, Jianqiang Sun, Anping Zhang, Shanshan Zhou
Summary: The study on the distribution patterns of OCPs in the surface sediments collected from Prydz Bay, Antarctica revealed that concentrations were mainly influenced by HCHs and DDTs, with a distinct quasiconcentric circle pattern controlled by total organic carbon and local hydrodynamic conditions. Source apportionment indicated that HCHs and chlordanes were primarily derived from long range atmospheric transport. Annual sedimentary fluxes of OCPs in Antarctica were one to three orders of magnitude lower than some data from the Arctic areas, implying a long active lifetime of OCPs in the Antarctic environment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Xiaoxia Bai, Qiang Xu, Hong Li, Cheng Cheng, Qiang He
Summary: This study reveals that damming of rivers alters the spatial distribution of carbon in sediments, leading to higher CH4 and CO2 concentrations upstream compared to downstream. During reservoir impounding periods, CH4 diffusive flux is higher upstream than downstream, while CH4 emissions are predominantly by ebullition, with significantly higher flux downstream during discharging periods. The increase in TOC in downstream sediment is attributed to riparian zone soil erosion caused by water level fluctuations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Cell Biology
Maria A. Dimitriu, Irina Lazar-Contes, Martin Roszkowski, Isabelle M. Mansuy
Summary: Recent advances in single-cell analyses have led to comprehensive characterization of cellular and molecular states, with the development of multiplexed assays offering simultaneous analysis of multiple factors and processes. These technologies have rapidly evolved, providing better specificity, precision, and resolution. This review summarizes recent progress in single-cell multiomics approaches, focusing on innovative techniques that integrate genome, epigenome, and transcriptome profiling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Connie Le, Yanming Liu, Joaquin Lopez-Orozco, Michael A. Joyce, X. Chris Le, D. Lorne Tyrrell
Summary: A CRISPR-Cas9 technique was developed to deplete high-abundance transcripts and enrich rare transcripts in single-cell RNA sequencing. Applying this technique to liver cells infected with HBV showed successful sequencing of HBV RNA in over 74% of the cells by depleting highly abundant transcripts. Single-cell RNA-seq analysis revealed that HBV infection did not significantly alter gene expression of host cells, while interferon treatment dramatically changed gene expression.
ANALYTICAL CHEMISTRY
(2021)
Review
Environmental Sciences
Sofia L. D'Ambrosio, John A. Harrison
Summary: This article provides a critical review of methods used to estimate the diffusive flux of CH4 from lake sediments, including incubation, benthic chambers, and modeling approaches. The limitations and advantages of each method are discussed, along with published comparisons between different methods. The article also highlights the need for the development and application of new methods to advance understanding of lake CH4 fluxes.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Ecology
Stephanie A. Carr, Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappe, Beth N. Orcutt
Review
Limnology
Beth N. Orcutt, James A. Bradley, William J. Brazelton, Emily R. Estes, Jacqueline M. Goordial, Julie A. Huber, Rose M. Jones, Nagissa Mahmoudi, Jeffrey J. Marlow, Sheryl Murdock, Maria Pachiadaki
LIMNOLOGY AND OCEANOGRAPHY
(2020)
Article
Ecology
Jessica K. Jarett, Maria Dzunkova, Frederik Schulz, Simon Roux, David Paez-Espino, Emiley Eloe-Fadrosh, Sean P. Jungbluth, Natalia Ivanova, John R. Spear, Stephanie A. Carr, Christopher B. Trivedi, Frank A. Corsetti, Hope A. Johnson, Eric Becraft, Nikos Kyrpides, Ramunas Stepanauskas, Tanja Woyke
Article
Microbiology
Christopher B. Trivedi, Blake W. Stamps, Graham E. Lau, Stephen E. Grasby, Alexis S. Templeton, John R. Spear
Article
Ecology
Elizabeth M. Fones, Daniel R. Colman, Emily A. Kraus, Ramunas Stepanauskas, Alexis S. Templeton, John R. Spear, Eric S. Boyd
Summary: Metagenome assembled genomes (MAGs) and single amplified genomes (SAGs) associated with two different Methanobacterium lineages were discovered in subsurface fracture waters of the Samail Ophiolite in Oman. Lineage Type I was prevalent in neutral pH waters, while lineage Type II was abundant in hydrogen-rich, hyperalkaline waters. The recent diversification of the Type II lineage into hyperalkaline waters was likely driven by selection imposed by CO2/oxidant availability.
Article
Biology
Victoria A. Petryshyn, Emily N. Junkins, Blake W. Stamps, Jake V. Bailey, Bradley S. Stevenson, John R. Spear, Frank A. Corsetti
Summary: This study examines the role of micro-organisms in modern stromatolite growth and finds that DNA sequences mainly originate from tenant or squatter communities, rather than the actual builders. It highlights the difficulty in interpreting the role of biology in stromatolite morphogenesis when removed from their environmental context.
Article
Microbiology
Chelsea L. Murphy, Andriy Sheremet, Peter F. Dun, John R. Spear, Ramunas Stepanauskas, Tanja Woyke, Mostafa S. Elshahed, Noha H. Youssef
Summary: The study conducted a thorough comparative genomic analysis of 108 genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum, revealing their specialization in methylotrophy and identification of an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds. The occurrence of multiple alkane hydroxylases and monooxygenases was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Members of Binatota were found to prefer terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
Article
Environmental Sciences
Alexis S. Templeton, Eric T. Ellison, Clemens Glombitza, Yuki Morono, Kaitlin R. Rempfert, Tori M. Hoehler, Spencer D. Zeigler, Emily A. Kraus, John R. Spear, Daniel B. Nothaft, Elizabeth M. Fones, Eric S. Boyd, Mason Munro-Ehrlich, Lisa E. Mayhew, Dawn Cardace, Juerg M. Matter, Peter B. Kelemen
Summary: The Oman Drilling Project established an Active Alteration multi-borehole observatory in peridotites undergoing low-temperature serpentinization in the Samail Ophiolite, where highly serpentinized rocks are in contact with strongly reducing fluids, hosting an active subsurface ecosystem. Distinct hydrological regimes, steep redox and pH gradients, and microbial activity were observed, with potential biogeochemical interactions leading to the formation of specific mineral assemblages as indicators of microbial life.
JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES
(2021)
Article
Microbiology
Patrick H. Thieringer, Alexander S. Honeyman, John R. Spear
Summary: The study focused on uniquely adapted microorganisms in the deep biosphere, the relationship between surface and subsurface microbial communities, and the dynamic nature of microbial composition in the near-subsurface. Additionally, the research explored the interconnectedness between surface influences and subsurface environments through geochemical processes.
MICROBIOLOGY SPECTRUM
(2021)
Article
Biotechnology & Applied Microbiology
Alexander S. Honeyman, Timothy S. Fegel, Henry F. Peel, Nicole A. Masters, David C. Vuono, William Kleiber, Charles C. Rhoades, John R. Spear
Summary: Wildfires are a global phenomenon that have uncertain effects on soil biogeochemical processes. In this study, wildfires in Colorado were examined and statistical learning was used to predict and explain the biogeochemical responses of soil. The results show that statistical learning can accurately predict these responses, with the inclusion of uncommon soil microbiota yielding the best predictions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Daniel R. Colman, Emily A. Kraus, Patrick H. Thieringer, Kaitlin Rempfert, Alexis S. Templeton, John R. Spear, Eric S. Boyd
Summary: Using genome-resolved metagenomics, researchers identified two deeply branching bacterial acetogen types in subsurface fracture water communities from the Samail Ophiolite in Oman. These findings provide insights into the ecological functions and metabolic characteristics of acetogens in contemporary serpentinizing systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Environmental Sciences
Alexander S. Honeyman, Theresa Merl, John R. Spear, Klaus Koren
Summary: The spatial responses of soil to fire are still unclear. Researchers used optical chemical sensing with planar 'optodes' to track pH and dissolved O2 concentrations in soil after burning and watering. The results showed that soil pH increased and dissolved O2 concentrations were not impacted until postfire watering. pH and dissolved O2 concentrations were negatively correlated with the relative expression of certain genes.
ENVIRONMENTAL RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Emily A. Kraus, Daniel Nothaft, Blake W. Stamps, Kaitlin R. Rempfert, Eric T. Ellison, Juerg M. Matter, Alexis S. Templeton, Eric S. Boyd, John R. Spear
Summary: The study explores the functional capability and activity of microbial methane cycling in serpentinization-impacted subsurface waters in the Samail Ophiolite of Oman. The results reveal active methanogenic and methanotrophic populations, particularly in waters with hyperalkaline pH. This highlights the potential for biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Emily N. Junkins, Blake W. Stamps, Frank A. Corsetti, Ronald S. Oremland, John R. Spear, Bradley S. Stevenson
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2019)
Article
Microbiology
Blake W. Stamps, John R. Spear
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)