Article
Microbiology
Edward F. DeLong
Summary: In 1977, Woese and Fox discovered a new microbial domain, Archaea, and later found that they were not only limited to extreme environments but also abundant in oxygen-rich marine waters. Subsequent studies revealed the widespread presence of marine planktonic archaea, their unexpected symbiotic associations, physiologies, and global abundance.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Kai P. Law, Wei He, Jianchang Tao, Chuanlun Zhang
Summary: Archaea are differentiated by the unique structure and composition of their lipids. Characterization of the lipidome remains technologically challenging due to the complexity and diversity of lipids. Developing novel analytical protocols is necessary to enhance lipidome coverage and provide insights into the adaptability of archaea to environmental stresses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Rob A. Schmitz, Nunzia Picone, Helena Singer, Andreas Dietl, Kerstin-Aniko Seifert, Arjan Pol, Mike S. M. Jetten, Thomas R. M. Barends, Lena J. Daumann, Huub J. M. Op den Camp
Summary: The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems characterized by high methane degassing and lanthanide concentrations. Lanthanides, essential in high-tech devices, are actively taken up by methanotrophs/methylotrophs due to their XoxF-type methanol dehydrogenases requiring lanthanides as metal cofactors. Purification and characterization of a neodymium-containing methanol dehydrogenase from Methylacidimicrobium thermophilum AP8 provide insights into lanthanide biochemistry.
Article
Microbiology
Shingo Kato, Masafumi Ohnishi, Mai Nagamori, Masahiro Yuki, Tomonori Takashina, Moriya Ohkuma, Takashi Itoh
Summary: A new thermoacidophilic, anaerobic, iron- and sulfur-reducing archaeon strain NAS-02(T) was isolated from a terrestrial hot spring in Japan, leading to the proposal of a new genus Conexivisphaera calida gen. nov., sp. nov. The establishment of the new family Conexivisphaeraceae fam. nov., order Conexivisphaerales ord. nov., and class Conexivisphaeria class. nov. also followed based on phylogenetic and physiological analysis.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Zhong Guo, Oleh Smutok, Wayne A. Johnston, Patricia Walden, Jacobus P. J. Ungerer, Thomas S. Peat, Janet Newman, Jake Parker, Tom Nebl, Caryn Hepburn, Artem Melman, Richard J. Suderman, Evgeny Katz, Kirill Alexandrov
Summary: The study aims to investigate the optimal strategy for developing artificial small molecule:protein complexes that function as chemically induced dimerization (CID) systems. By using methotrexate-controlled CID systems, the critical role of drug-induced conformational change in ligand-controlled protein complex assembly is revealed. The utility of the developed CID is demonstrated by constructing an electrochemical biosensor of methotrexate for quantification in human serum, as well as developing a multiplexed bioelectronic system for repeated measurements of multiple analytes using methotrexate and functionally related biosensor of rapamycin.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Parsifal F. Islas-Morales, Anny Cardenas, Maria J. Mosqueira, Luis Felipe Jimenez-Garcia, Christian R. Voolstra
Summary: Nucleoli are subcellular compartments responsible for transcription and maturation of pre-ribosomal RNAs. This study provides evidence for the presence of nucleolus-like subcellular domains in TACK crenarchaeon Saccharolobus solfataricus, suggesting that these domains are not exclusive to eukaryotes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Elena Vortsepneva, Pierre Chevaldonne, Alexandra Klyukina, Elizaveta Naduvaeva, Christiane Todt, Anna Zhadan, Alexander Tzetlin, Ilya Kublanov
Summary: The study presents a new species of Solenogastres, Tegulaherpia sp., discovered in Mediterranean marine caves. The transparent mollusks were found to harbor a variety of microbial cells on their surface, including bacteria and archaea. These microbes, similar to those associated with other marine animals, are believed to play a role in nitrogen metabolism and biopolymer decomposition.
Review
Biochemical Research Methods
Zhiguang Zhu, Haiyan Song, Yuanming Wang, Yi-Heng P. J. Zhang
Summary: The development of electrochemical biosensors has received significant attention, with protein engineering being used to enhance the properties of redox enzymes for applicable biosensors. This review focuses on recent advances in protein engineering for improving enzymatic catalysis, facilitating electron transfer and enzyme immobilization, and constructing allosteric protein biosensors. The pros and cons of different protein engineering strategies are briefly discussed, along with future perspectives.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Microbiology
Anna N. Rasmussen, Christopher A. Francis
Summary: Ammonia-oxidizing archaea (AOA) play a crucial role in the transformation of ammonia in aquatic environments worldwide, especially in nutrient-rich coastal and estuarine waters like San Francisco Bay. A study found a significant AOA bloom in the southern part of San Francisco Bay, which coincided with high nitrite concentrations. Analysis of AOA genomes revealed their streamlined structure and specific genomic characteristics. These findings provide important insights into the understanding of AOA blooms.
Article
Food Science & Technology
Yang Wang, Donglei Zhao, Wei Zhang, Songxue Wang, Kai Huang, Baoyuan Guo
Summary: A bacterial consortium named SD, consisting of Pseudomonas sp. SD17-1 and Devosia sp. SD17-2, was isolated from Tenebrio molitor larvae feces, and it has the ability to oxidize deoxynivalenol (DON) to 3-keto-DON. The optimal conditions for the DON oxidation activity of SD were found to be a temperature of 30 ?C, a pH of 8.0-9.0, and an initial inoculum ratio of Devosia to Pseudomonas of 0.1. Pseudomonas was responsible for producing the necessary PQQ cofactor, while Devosia expressed the PQQ-dependent DON dehydrogenase, together facilitating the oxidation of DON.
Article
Multidisciplinary Sciences
Ronnakrit Rattanasriampaipong, Yi Ge Zhang, Ann Pearson, Brian P. Hedlund, Shuang Zhang
Summary: Archaeal membrane lipids, specifically the GDGTs, can be used to reconstruct ancient temperatures and provide insights into the ecology and evolution of marine ammonia-oxidizing archaea (AOA). The study identified thermal and nonthermal behaviors of GDGTs, which can be used as indicators of environmental temperature. The distribution of GDGTs in AOA cultures and shallow water samples followed a temperature-dependent trend, while deep water samples showed a nonthermal behavior. Statistical analysis revealed long-term trends in GDGT-2/GDGT-3 ratios, suggesting a suppression of deep water marine AOA during greenhouse climates in the Mesozoic and early Cenozoic periods.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Dennis Winkler, Sabrina Gfrerer, Johannes Gescher
Summary: The physiology of acidophilic Micrarchaeota, such as Candidatus Micrarchaeum harzensis A_DKE, remains largely unknown due to the highly expressed hypothetical proteins. In this study, isocitrate dehydrogenase (MhIDH) from A_DKE was recombinantly produced and characterized, showing specific activity for NADP(+) with low affinity likely due to a proline residue in the NADP(+) binding pocket.
Article
Chemistry, Analytical
Paulina K. Wells, Oleh Smutok, Zhong Guo, Kirill Alexandrov, Evgeny Katz
Summary: Advances in protein engineering have made it possible to create protein biosensors as alternatives to analytical and diagnostic methods. This study focuses on the construction of a protein biosensor array using an artificial variant of PQQ-glucose dehydrogenase, which addresses the challenges of sensitivity, multiplexing, and manufacturability. By immobilizing GDH protein on silica nanoparticles and monitoring changes in fluorescence, a highly sensitive biosensor array with low background and a wide dynamic range has been successfully developed for quantitative detection of drugs in biological fluids.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Likui Zhang, Donghao Jiang, Yuting Li, Leilei Wu, Qing Liu, Kunming Dong, Philippe Oger
Summary: Tba ADH(547) is a thermoactive alcohol dehydrogenase that can oxidize ethanol and reduce acetaldehyde at high temperature with similar optimal temperature and thermostability, but different optimal pH for oxidation and reduction. It is dependent on a divalent ion for oxidation activity and shows substrate preference for certain alcohols.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Microbiology
Tatsunori Nakagawa, Mori Koji, Akira Hosoyama, Atsushi Yamazoe, Yuki Tsuchiya, Shingo Ueda, Reiji Takahashi, David A. Stahl
Summary: Strain NM25T is a novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota. It has rod-shaped cells with an S-layer cell wall, and utilizes ammonia oxidation for energy. It is most closely related to Nitrosopumilus ureiphilus PS0T, with genome relatedness of 85.4% based on average nucleotide identity. The strain represents a new species of the genus Nitrosopumilus.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Ecology
Daniel Muratore, Angela K. Boysen, Matthew J. Harke, Kevin W. Becker, John R. Casey, Sacha N. Coesel, Daniel R. Mende, Samuel T. Wilson, Frank O. Aylward, John M. Eppley, Alice Vislova, Shengyun Peng, Rogelio A. Rodriguez-Gonzalez, Stephen J. Beckett, E. Virginia Armbrust, Edward F. DeLong, David M. Karl, Angelicque E. White, Jonathan P. Zehr, Benjamin A. S. Van Mooy, Sonya T. Dyhrman, Anitra E. Ingalls, Joshua S. Weitz
Summary: By integrating time series analyses of different molecules, the authors demonstrate that microorganisms in the open ocean partition scarce resources temporally, with different microbial groups expressing nitrogen uptake and assimilation processes at different points throughout the day and night cycle. Despite competition for limited nutrients, high taxonomic diversity of microbes in the surface ocean still persists, which challenges ecological theory. The study reveals temporal niche partitioning of nitrogen assimilation processes, with different microbial groups exhibiting asynchronous transcription of genes involved in nitrogen uptake.
NATURE ECOLOGY & EVOLUTION
(2022)
Review
Microbiology
Mary Ann Moran, Elizabeth B. Kujawinski, William F. Schroer, Shady A. Amin, Nicholas R. Bates, Erin M. Bertrand, Rogier Braakman, C. Titus Brown, Markus W. Covert, Scott C. Doney, Sonya T. Dyhrman, Arthur S. Edison, A. Murat Eren, Naomi M. Levine, Liang Li, Avena C. Ross, Mak A. Saito, Alyson E. Santoro, Daniel Segre, Ashley Shade, Matthew B. Sullivan, Assaf Vardi
Summary: This article reviews the sources, roles, and methods of analysis for microbial metabolites in the surface ocean.
NATURE MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Frank O. Aylward, Mohammad Moniruzzaman
Summary: Discoveries over the last century have shown that viruses can be surprisingly complex in terms of their physical structures, genomic organization, ecological interactions, and evolutionary histories. They can have physical dimensions and genome lengths that surpass many cellular lineages, and their infection strategies often involve significant remodeling of their host cells. Virus-virus communication and hyperparasitism are common in the virosphere, contributing to their success. The study of large DNA viruses is particularly important for understanding viral complexity and future research directions.
Article
Limnology
Barbara Bayer, Kelsey McBeain, Craig A. Carlson, Alyson E. Santoro
Summary: Nitrifying microorganisms in the ocean play a crucial role in the global carbon cycle by fixing dissolved inorganic carbon into biomass and releasing organic compounds for marine food webs. Our study provides measurements of DOC release by marine nitrifiers, which contribute to the understanding of the global carbon cycle and carbon sequestration in the ocean.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Article
Virology
Mohammad Moniruzzaman, Maria P. Erazo-Garcia, Frank O. Aylward
Summary: This study discovered the presence of endogenous giant viruses in Chlamydomonas reinhardtii, which has important implications for understanding the genetic characteristics and population dynamics of this alga.
Editorial Material
Multidisciplinary Sciences
Mohammad Moniruzzaman, Frank O. Aylward
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Justus Niemeyer, Laura Fischer, Frank O'Neill Aylward, Michael Schroda
Summary: This study investigated the use of promoters from giant virus genomes in Chlamydomonas reinhardtii to drive gene expression. The results showed that the viral promoters were unable to effectively drive gene expression. Additionally, it was found that by mutating the start codons of mCherry and using the 5 '-UTR of beta TUB2, the problem of gene expression in Chlamydomonas could be overcome.
Correction
Microbiology
Angela K. Boysen, Laura T. Carlson, Bryndan P. Durham, Ryan D. Groussman, Frank O. Aylward, Francois Ribalet, Katherine R. Heal, Angelicque E. White, Edward F. DeLong, E. Virginia Armbrust, Anitra E. Ingalls
Article
Virology
Frank O. Aylward, Jonatas S. Abrahao, Corina P. D. Brussaard, Matthias G. Fischer, Mohammad Moniruzzaman, Hiroyuki Ogata, Curtis A. Suttle
Summary: Recent taxonomic updates have been made for giant viruses in the order Imitervirales, including the creation of new families and subfamilies, as well as the adoption of binomial names for all recognized species.
ARCHIVES OF VIROLOGY
(2023)
Article
Environmental Sciences
Noah Gluschankoff, Alyson E. Santoro, Carolyn Buchwald, Karen L. Casciotti
Summary: The El Nino-Southern Oscillation (ENSO) is a natural climate phenomenon that affects the biogeochemical and physical dynamics of the Eastern Tropical Pacific Ocean. The two phases of ENSO, El Nino and La Nina, have cascading effects on primary productivity, organic matter supply, and ocean-atmosphere interactions.
GLOBAL BIOGEOCHEMICAL CYCLES
(2023)
Article
Ecology
Anh D. D. Ha, Mohammad Moniruzzaman, Frank O. O. Aylward
Summary: Viruses of the phylum Nucleocytoviricota are widespread in ocean waters and have important impacts on marine ecosystems. This study used metagenomic data to investigate the biogeography of these viruses and found that they are most abundant in shallow waters. The study also identified latitudinal patterns in viral diversity, with the highest diversity observed at high latitudes in the northern hemisphere. These results contribute to our understanding of the distribution and diversity of viruses in marine systems.
ISME COMMUNICATIONS
(2023)
Article
Ecology
Alaina R. Weinheimer, Frank O. Aylward, Matthieu Leray, Jarrod J. Scott
Summary: Phages play a crucial role in controlling microbial communities by selectively infecting and killing cells. The composition of phage communities is primarily shaped by dispersal processes, while prokaryotes are more influenced by local conditions.
ISME COMMUNICATIONS
(2023)
Review
Microbiology
Mohammad Moniruzzaman, Maria Paula Erazo Garcia, Roxanna Farzad, Anh D. Ha, Abdeali Jivaji, Sangita Karki, Uri Sheyn, Joshua Stanton, Benjamin Minch, Danae Stephens, Dustin C. Hancks, Rodrigo A. L. Rodrigues, Jonatas S. Abrahao, Assaf Vardi, Frank O. Aylward
Summary: The phylum Nucleocytoviricota includes the largest and most complex viruses known, with a long evolutionary history. These viruses manipulate the physiology of their hosts, including through mimicry and the acquisition of various functional genes. Understanding the roles of viral genes during infection and how viruses acquire complex functional repertoires are important areas of research in giant virus studies.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Ecology
Emily J. Zakem, Barbara Bayer, Wei Qin, Alyson E. E. Santoro, Yao Zhang, Naomi M. Levine
Summary: This study uses a mechanistic microbial ecosystem model to derive simple expressions for the controls on ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in the deep ocean. It finds that the supply of ammonium, not the traits of AOA or NOB, determines the ammonia and nitrite oxidation rates in the water column, and that the relative yields of AOA and NOB alone set their relative bulk carbon fixation rates.
Article
Education & Educational Research
Meredith G. Meyer, Weida Gong, Sile M. Kafrissen, Olivia Torano, Diana E. Varela, Alyson E. Santoro, Nicolas Cassar, Scott Gifford, Alexandria K. Niebergall, Garrett Sharpe, Adrian Marchetti
Summary: The NASA EXPORTS program aims to understand global carbon export efficiency. The study conducted in the Northeast Pacific Ocean in summer 2018 revealed low phytoplankton biomass dominated by small cells reliant on recycled nutrients. The findings highlight the importance of small cells in primary and new production and the moderate productivity fluctuations in this region.
INTERNATIONAL JOURNAL OF DISTANCE EDUCATION TECHNOLOGIES
(2022)