Article
Multidisciplinary Sciences
Minchung Kang, Geeta Chhetri, Inhyup Kim, Yoonseop So, Taegun Seo
Summary: In this study, four novel bacterial strains belonging to the genus Ramlibacter were isolated from different environments in Busan and Jeju Island, Republic of Korea. Strain USB13(T) showed cellulolytic activity, making it the first within its genus to possess this property. Comparative analysis of their genomes revealed differences in G + C contents and genome sizes. Based on polyphasic evidence, four new species within the genus Ramlibacter were proposed.
SCIENTIFIC REPORTS
(2022)
Article
Soil Science
Dorota L. Porazinska, Clifton P. Bueno de Mesquita, Emily C. Farrer, Marko J. Spasojevic, Katharine N. Suding, Steven K. Schmidt
Summary: Climate warming drives shifts in nematode communities at Niwot Ridge in the Colorado Rocky Mountains, with changes in plant cover influencing the diversity and density of nematodes. These shifts are associated with changes in soil carbon and nitrogen levels.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Ecology
Madhav P. Thakur, Wim H. van Der Putten, Fariha Apon, Ezio Angelini, Branko Vres, Stefan Geisen
Summary: Climate change can disrupt food chains, affecting predator-prey relationships in microbial communities. Extreme heat events can have a more detrimental impact on microbial prey communities than on their predators, possibly due to thermal acclimation mechanisms in predators. The resilience of predators and prey in rhizosphere microbial communities may vary based on species-specific effects and time dynamics.
FUNCTIONAL ECOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Brendan Epstein, Liana T. Burghardt, Katy D. Heath, Michael A. Grillo, Adam Kostanecki, Tuomas Hamala, Nevin D. Young, Peter Tiffin
Summary: This study investigated the coevolution between legumes and rhizobia using population genomic analysis. The results showed that there were genotype-by-genotype effects on rhizobial fitness and some rhizobial genes displayed signatures of recent positive selection. However, neither annotated host symbiosis genes nor genes responsible for this variation showed enrichment for positive or balancing selection. This suggests that stabilizing selection dominates the selection acting on symbiotic traits, and the variation in these traits is under mutation-selection balance. Furthermore, the study found that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.
Article
Biotechnology & Applied Microbiology
Per Johansson, Elina Sade, Jenni Hultman, Petri Auvinen, Johanna Bjorkroth
Summary: Genomic analysis of 37 strains of Leuconostoc gelidum and Leuconostoc gasicomitatum supports the reclassification of L. gelidum subsp. gasicomitatum to L. gasicomitatum at the species level. The study also revealed limited intraspecies variation in genome properties, which were not attributed to the source of isolation. Additionally, none of the strains carried acquired antimicrobial resistance genes or genes associated with virulence, indicating the lack of functional and phylogenetic diversification driving their distribution and lifestyle in foods.
Article
Ecology
Caylon F. Yates, Ryan Trexler, Idalys Bonet, William L. King, Kevin L. Hockett, Terrence H. Bell
Summary: The realized niche breadth of soil microorganisms is typically smaller than their fundamental niche breadth due to competition. By conditioning bacterial isolates to biotically cleared soils, niche breadth expansion can be achieved, but the extent of niche shifts varies among different bacteria populations.
FUNCTIONAL ECOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Fatemeh Khani-Juyabad, Parisa Mohammadi, Mahboobeh Zarrabi
Summary: Phylogenomic analysis of Nostocsp. MG11, a terrestrial cyanobacterium, and other terrestrial and freshwater Nostoc strains reveals that terrestrial strains have larger genomes supported by an increase in core gene copy numbers and acquisition of shared genes. Transcriptomic analysis under desiccation stress shows that Nostoc sp. MG11 protects its cells and maintains normal metabolism through the up-regulation of specific genes related to stress response and metabolic processes.
Article
Agriculture, Dairy & Animal Science
Hanpeng Luo, Xiang Li, Lirong Hu, Wei Xu, Qin Chu, Aoxing Liu, Gang Guo, Lin Liu, Luiz F. Brito, Yachun Wang
Summary: Heat stress is a major issue in the global dairy cattle industry, and genetic selection for heat tolerance can have a positive impact. This study identified key genetic factors related to rectal temperature in Holstein cattle and validated candidate genes influencing heat stress response.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Multidisciplinary Sciences
Yifei Sun, Chengyuan Tao, Xuhui Deng, Hongjun Liu, Zongzhuan Shen, Yaxuan Liu, Rong Li, Qirong Shen, Stefan Geisen
Summary: The soil bacterial microbiome plays a crucial role in ecosystem functioning. Organic fertilization can enhance the resistance and resilience of bacterial communities in extreme drought and subsequent rewetting compared to conventional fertilizers. This study indicates that organic fertilization can enhance the stability of the soil microbiome and ensure the recovery of specific bacterial-driven ecosystem functions after rewetting.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Oncology
Setor Amuzu, Euridice Carmona, Anne-Marie Mes-Masson, Celia M. T. Greenwood, Patricia N. Tonin, Jiannis Ragoussis
Summary: Olaparib is an oral medication used to treat certain advanced ovarian and breast cancers with mutations in BRCA1 or BRCA2 genes. Additional gene alterations may increase sensitivity to olaparib. Further experimental and clinical investigations are needed to validate these findings.
Article
Geography, Physical
Joseph S. Levy, Bronson Cvijanovich
Summary: Ice-cemented permafrost can provide bank cohesion, resulting in meandering single-threaded rivers, which can also be found in non-vegetated environments. Previous studies could not determine the relative impact of frozen sediments or roots on bank cohesion due to the presence of bank vegetation in most permafrost sites. This study on an unvegetated, ice-cemented permafrost river in Antarctica shows that meandering river processes can occur in such environments, with bank cohesion provided by ice-cemented permafrost.
Article
Microbiology
Alexa M. Nicolas, Alexander L. Jaffe, Erin E. Nuccio, Michiko E. Taga, Mary K. Firestone, Jillian F. Banfield
Summary: This study focused on Candidate Phyla Radiation (CPR) bacteria and DPANN archaea in soil, which are often overlooked. By concentrating small particles from soil, the researchers were able to identify these organisms as part of the rare soil biosphere with unique metabolic platforms. Some of these predicted symbionts have acquired aerobic capacity through lateral transfer, enabling them to adapt to oxic soil environments.
Article
Microbiology
Xiuping Liu, Lu Lyu, Jiaqian Li, Biswarup Sen, Mohan Bai, Jason E. Stajich, Jackie L. Collier, Guangyi Wang
Summary: This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains and investigates their ecological functions from the perspective of organic matter degradation using comparative genomics and biochemical assays. The results show that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems and can actively participate in marine biochemical cycles as decomposers. The study also emphasizes the dual roles of endoglucanase in the process of cellulose degradation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Soil Science
Bing-Bing Li, Sarah S. Roley, David S. Duncan, Jiarong Guo, John F. Quensen, Han-Qing Yu, James M. Tiedje
Summary: This study found that nitrogen fertilizer has an impact on soil microbial community structure and interaction, especially with long-term excess application. The fertilizer promoted certain metabolic processes while reducing other traits, making microbial networks more sensitive to environmental changes.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Ryota Yamano, Juanwen Yu, Chunqi Jiang, Alfabetian Harjuno Condro Haditomo, Sayaka Mino, Yuichi Sakai, Tomoo Sawabe
Summary: A novel bacterium strain PT3(T) was isolated from the larvae of the Japanese sea cucumber, and phylogenetic analysis showed that it belongs to a new genus Aliamphritea, separate from Amphritea ceti and Amphritea spongicola.
Article
Biotechnology & Applied Microbiology
Emad A. Albakistani, Felix C. Nwosu, Chantel Furgason, Evan S. Haupt, Angela Smirnova, Tobin J. Verbeke, Eun-Suk Lee, Joong-Jae Kim, Amelia Chan, Ilona A. Ruhl, Andriy Sheremet, Sarah B. Rudderham, Matthew B. J. Lindsay, Peter F. Dunfield
Summary: This study examined the methanotrophic bacteria in an industrial end pit lake using molecular DNA methods combined with biogeochemical measurements. The results showed clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that temperature based niche partitioning is a major control for this succession. This study helps to understand microbial dynamics in engineered end pit lakes and has implications for microbial ecology and limnology.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Robert M. Bowers, Stephen Nayfach, Frederik Schulz, Sean P. Jungbluth, Ilona A. Ruhl, Andriy Sheremet, Janey Lee, Danielle Goudeau, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Rex R. Malmstrom, Nikos C. Kyrpides, Peter F. Dunfield, Tanja Woyke
Summary: Advancements in single-cell genomics have enabled rapid and affordable sequencing of microbial communities, providing a comprehensive snapshot of community composition and function. This approach also allows for the direct linkage of mobile elements to hosts and analysis of population heterogeneity among dominant community members.
Article
Biochemistry & Molecular Biology
Grayson L. Chadwick, Connor T. Skennerton, Rafael Laso-Perez, Andy O. Leu, Daan R. Speth, Hang Yu, Connor Morgan-Lang, Roland Hatzenpichler, Danielle Goudeau, Rex Malmstrom, William J. Brazelton, Tanja Woyke, Steven J. Hallam, Gene W. Tyson, Gunter Wegener, Antje Boetius, Victoria J. Orphan
Summary: The anaerobic oxidation of methane coupled to sulfate reduction is a microbial process that involves a partnership between anaerobic methanotrophic archaea and sulfate-reducing bacteria. This study reconstructed and analyzed 28 ANME genomes, enabling a comparative analysis of all marine ANME clades. The findings suggest that methane production may have evolved from a methanotrophic ancestor.
Article
Biotechnology & Applied Microbiology
Hannah D. Schweitzer, Heidi J. Smith, Elliott P. Barnhart, Luke J. McKay, Robin Gerlach, Alfred B. Cunningham, Rex R. Malmstrom, Danielle Goudeau, Matthew W. Fields
Summary: This study investigates the potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams from the Powder River Basin using environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes. The results reveal the presence of biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways in the active populations across the sampled coal seams.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Geochemistry & Geophysics
Xin Jin, Yuki Tomimatsu, Runsheng Yin, Tetsuji Onoue, Marco Franceschi, Stephen E. Grasby, Yixing Du, Manuel Rigo
Summary: The Carnian Pluvial Episode (CPE) was characterized by various changes in carbon isotope, biota, and climate. The possible link between the CPE and the Wrangellia Large Igneous Province (Wrangellia LIP) activity remains unclear. The study presents evidence of excess mercury loading in sediments and suggests that variations in Wrangellia LIP volcanism may have driven biotic and climate changes during the CPE.
EARTH AND PLANETARY SCIENCE LETTERS
(2023)
Article
Multidisciplinary Sciences
Julia Anstett, Alvaro M. Plominsky, Edward F. DeLong, Alyse Kiesser, Klaus Juergens, Connor Morgan-Lang, Ramunas Stepanauskas, Frank J. Stewart, Osvaldo Ulloa, Tanja Woyke, Rex Malmstrom, Steven J. Hallam
Summary: Oxygen-deficient marine waters known as OMZs or AMZs are common oceanographic features that host microorganisms adapted to low oxygen conditions. The metabolic interactions of these microorganisms drive biogeochemical cycles and impact nitrogen loss and trace gas production and consumption. With the expansion and intensification of oxygen-deficient waters due to global warming, studying microbial communities in these areas is important for understanding the effects of climate change on marine ecosystem functions and services.
Article
Geosciences, Multidisciplinary
Kunyue Ling, Hanjie Wen, Haifeng Fan, Xiangkun Zhu, Zhihong Li, Zhengwei Zhang, Stephen E. Grasby
Summary: The bauxites in southwestern China during the early Carboniferous period have extremely low iron content, indicating significant iron loss during continental weathering. This finding is crucial for understanding global iron cycling and marine ecosystems.
JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE
(2023)
Article
Geochemistry & Geophysics
Yaowen Wu, Hui Tian, Runsheng Yin, Di Chen, Stephen E. Grasby, Jun Shen, Tengfei Li, Sui Ji, Ping'an Peng
Summary: New geochemical data on mercury isotopes suggest that the redox state of shallow water environments in the Mesoproterozoic era was more dynamic and complex than previously thought, and this condition may have significantly influenced the diversification of organisms.
EARTH AND PLANETARY SCIENCE LETTERS
(2023)
News Item
Microbiology
Rex R. Malmstrom
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ranjani Murali, Hang Yu, Daan R. Speth, Fabai Wu, Kyle S. Metcalfe, Antoine Cremiere, Rafael Laso-Perez, Rex R. Malmstrom, Danielle Goudeau, Tanja Woyke, Roland Hatzenpichler, Grayson L. Chadwick, Stephanie A. Connon, Victoria J. Orphan
Summary: This study investigated the metabolic adaptation of sulfate-reducing bacteria (SRB) in the syntrophic partnership with anaerobic methanotrophic archaea (ANME) using comparative metagenomics and phylogenetics. The results showed that the protein complexes involved in direct interspecies electron transfer (DIET) were conserved between syntrophic lineages, while the proteins involved in electron transfer within the SRB inner membrane differed. Unique adaptations were also found within syntrophic SRB clades, which varied depending on the archaeal partner.
Article
Microbiology
Ryan V. Trexler, Marc W. Van Goethem, Danielle Goudeau, Nandita Nath, Rex R. Malmstrom, Trent R. Northen, Estelle Couradeau
Summary: Determining the active microorganisms in soil communities is key in microbial ecology research. This study applied the BONCAT-FACS-Seq method to profile the diversity and potential functions of active and inactive microorganisms in a biocrust community after rain. The results showed that BONCAT-FACS-Seq can discern the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active fraction of the biocrust community is characterized by taxa commonly observed in other biocrust communities.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Dariia Vyshenska, Pranav Sampara, Kanwar Singh, Andy Tomatsu, W. Berkeley Kauffman, Erin E. Nuccio, Steven J. Blazewicz, Jennifer Pett-Ridge, Katherine B. Louie, Neha Varghese, Matthew Kellom, Alicia Clum, Robert Riley, Simon Roux, Emiley A. Eloe-Fadrosh, Ryan M. Ziels, Rex R. Malmstrom
Summary: Answering the questions, who is eating what? and who is active? within complex microbial communities is essential for modeling, predicting, and modifying microbiomes for improved human and planetary health. Stable isotope probing can be used to track the incorporation of labeled compounds into cellular DNA during microbial growth to address these questions. However, traditional stable isotope methods face challenges in establishing links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. This study presents an experimental and analytical workflow that improves the detection of metabolically active microorganisms and provides better quantitative estimates of genome-resolved isotope incorporation, thus refining ecosystem-scale models for carbon and nutrient fluxes within microbiomes.
Article
Astronomy & Astrophysics
Kezhen Hu, Xiaojun Liu, Zhuoheng Chen, Stephen E. Grasby
Summary: Accurate estimation of mineral composition is crucial for refined reservoir characterization, thermal conductivity, and mechanical determinations of sedimentary rocks, especially in shale units. A hybrid machine learning approach enables the accurate description of mineralogical compositions across a basin, which has important implications for thermal conductivity modeling, reservoir evaluation, and extensive geological studies.
EARTH AND SPACE SCIENCE
(2023)
Article
Cell Biology
Rekha Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Dan Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rudiger Pukall, James R. White, Neha J. Varghese, Cody Webb, Krishnaveni Palaniappan, Lorenz C. Reimer, Joaquim Sarda, Jonathon Bertsch, Supratim Mukherjee, T. B. K. Reddy, Patrick P. Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong-Yen Wu, Zhiying Zhao, Yuguang Zhou, Lyudmila Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe-Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans-Peter Klenk, Tanja Woyke, Markus Goeker, Nikos C. Kyrpides, Natalia N. Ivanova
Summary: The study presents a comprehensive analysis of actinobacterial diversity, showing that only a small portion of this diversity is represented by sequenced genomes. The comparison of gene functions reveals novel determinants of host-microbe interaction and environment-specific adaptations. The analysis of biosynthetic gene clusters highlights the role of horizontal gene transfer and gene loss in shaping secondary metabolite repertoire.