Article
Biotechnology & Applied Microbiology
Hiroaki Naka, Margo G. Haygood
Summary: Teredinibacter turnerae is an intracellular bacterial symbiont found in shipworm gills, which produces turnerbactin to obtain iron for survival. The turnerbactin biosynthetic genes are conserved among T. turnerae strains. However, the mechanisms of Fe(III)-turnerbactin uptake are not fully understood.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Hiroshi Arai, Takumi Takamatsu, Shiou-Ruei Lin, Tetsuya Mizutani, Tsutomu Omatsu, Yukie Katayama, Madoka Nakai, Yasuhisa Kunimi, Maki N. Inoue
Summary: Many microbes induce male killing (MK) in various insect species, but it is not clear whether they adopt similar or different MK mechanisms. Researchers found that Wolbachia and Spiroplasma disrupt the sex determination cascade by inducing female-type splice variants of doublesex in male insects. In addition, Wolbachia and Spiroplasma also trigger abnormal apoptosis in male embryos.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Martina Prazeres, T. Edward Roberts, Shadrina Fildzah Ramadhani, Steve S. Doo, Christiane Schmidt, Marleen Stuhr, Willem Renema
Summary: The study found that local habitat is the main factor influencing the overall composition of the algal symbiont community, while host identity and phylogenetic relationship among hosts are also relevant in shaping the specific endosymbiont diatom community. The ability of Amphistegina species to associate with a diverse array of diatoms and possibly other algal groups likely underpins the ecological success of these crucial calcifying organisms across their extensive geographic range.
Article
Cell Biology
Na-Na Li, Shan Jiang, Kun-Yu Lu, Ji-Sheng Hong, Yan-Bin Wang, Jin-Yang Yan, Jun-Bo Luan
Summary: This study reveals how insect sex affects the development of bacteriocytes through cellular and molecular mechanisms. In the whitefly Bemisia tabaci, bacteriocytes in females undergo cell division, while bacteriocytes in males degenerate through autophagy and apoptosis. A transcription factor called Adf-1 plays a crucial role in this process.
Article
Ecology
Puspendu Sardar, Vladimir Sustr, Alica Chronakova, Frantisek Lorenc
Summary: Millipedes play a crucial role in decomposing soil organic matter, with their gut microbiota playing a key role in lignocellulose decomposition, while endogenous enzymes primarily handle digestion.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Applied
Cassie R. Bakshani, Fiona Cuskin, Neil J. Lant, Hamish C. L. Yau, William G. T. Willats, J. Grant Burgess
Summary: This study used molecular probe-based technologies to investigate the composition and relative abundance of glycans in burnt-on/baked-on (BoBo) food soil and identify enzymes that can facilitate soil breakdown. The results suggest that inclusion of xylan depolymerising enzymes in automatic dishwashing detergents may improve the cleaning of recalcitrant, plant glycan-rich BoBo soils. This study provides new insights into the composition and removal chemistry of complex, multi-component food soils.
Article
Environmental Sciences
Shuangshuang Ma, Hongtao Liu
Summary: In this study, a 3D-printed bulking agent with a uniform shape was prepared and its application in swine manure aerobic composting was investigated. The results showed that the addition of 3D-printed bulking agents can improve temperature, extend the thermophilic period, and enhance organic matter degradation, thus positively impacting the safety of compost products.
Article
Microbiology
Hiroshi Arai, Maki N. Inoue, Daisuke Kageyama
Summary: This study analyzed the genome and characteristics of a male-killing S. ixodetis strain in a moth species. The strain showed different genetic features compared to other strains and distributed systemically within the host. Additionally, the strain could infect distantly related insects. These findings reveal distinct origins and characteristics of S. ixodetis- and S. poulsonii-induced male-killing.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kristian Barrett, Cameron J. Hunt, Lene Lange, Igor Grigoriev, Anne S. Meyer
Summary: Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. The peptide-based clustering method CUPP provides further delineation of these enzymes by defining small protein groups with shared sequence motifs. The updated CUPP-webserver includes all published fungal and algal genomes from the Joint Genome Institute, allowing users to browse for specific predicted functions or protein families.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Wanrong Dong, Xiuling Ji, Yuhong Huang, Yaju Xue, Boxia Guo, Dongbo Cai, Shouwen Chen, Suojiang Zhang
Summary: This study presents a complete synthetic pathway for the direct conversion of CO2 to ethanol. The pathway consists of three functional modules and operates in a carbon-conserved and ATP-independent system. The efficiency of the pathway was enhanced by screening efficient enzymes and using a two-step reaction. The feasibility of converting CO2 to ethanol was demonstrated through experiments.
Article
Microbiology
Lu-Lu Meng, Rui-Cheng Liu, Liu Yang, Ying-Ning Zou, Anoop Kumar Srivastava, Kamil Kuca, Abeer Hashem, Elsayed Fathi Abd-Allah, Bhoopander Giri, Qiang-Sheng Wu
Summary: The study demonstrated that P. indica significantly increased fructose, glucose, and sucrose content in both leaves and roots of trifoliate orange, as well as influenced the concentration of certain unsaturated and saturated fatty acids. In contrast, F. mosseae inoculation had a minor impact on the fatty acid content, only increasing the content of certain fatty acids.
Article
Biochemistry & Molecular Biology
Anshul Sharma, Neha Sharma, Deepshikha Gupta, Hae-Jeung Lee, Young-Seo Park
Summary: Leuconostoc strains have great biotechnological potential due to their genomic features. In this study, the genomic diversity of four Leuconostoc strains was analyzed, revealing the sharing and differences of genes among the strains. The study also provided insights into the distribution of carbohydrate-active enzyme genes and genes with unknown functions, as well as the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc strains.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Anshul Sharma, Neha Sharma, Deepshikha Gupta, Hae-Jeung Lee, Young-Seo Park
Summary: This study identified and analyzed the genomic features of four Leuconostoc strains, revealing their genetic diversity and differences. The results showed a significant number of shared genes among the strains but varying gene content. Additionally, the study elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. These findings provide valuable information for the exploitation and utilization of these strains.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Organic
Gregor Tegl, Peter Rahfeld, Katharina Ostmann, John Hanson, Stephen G. Withers
Summary: Functional screening of a metagenomic library derived from a human gut microbiome led to the identification of four active HexNAcase candidates belonging to CAZy family GH20, with the generation of two new thioglycoligases through detailed kinetic analysis. This work demonstrates the rapid development of useful glycoside-forming mutants of HexNAcases, diversifying the pool of biocatalysts for carbohydrate synthesis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Microbiology
Barbara Maciejewska, Flavia Squeglia, Agnieszka Latka, Mario Privitera, Sebastian Olejniczak, Paulina Switala, Alessia Ruggiero, Daniela Marasco, Eliza Kramarska, Zuzanna Drulis-Kawa, Rita Berisio
Summary: This study investigates the structure and function of the capsular depolymerase KP34gp57 from Klebsiella phage KP34. The key catalytic residues were determined and the role of each domain in stability and catalytic activity was dissected. Surprisingly, C-terminally trimmed KP34gp57 variants were found to exist as monomers with full catalytic activity. This finding is innovative as it has not been observed before in phage depolymerases.
Article
Immunology
Gina M. Gallego-Lopez, Carolina Mendoza Cavazos, Andres M. Tibabuzo Perdomo, Andrew L. Garfoot, Roberta M. O'Connor, Laura J. Knoll
Summary: Chronic infection of the parasite Toxoplasma gondii provides protection against lethal secondary infection with other pathogens. In this study, soluble T. gondii antigens (STAg) were tested as a therapeutic for the parasite Cryptosporidium parvum. The results showed that STAg treatment reduced C. parvum oocyst shedding in mice, indicating its potential as a treatment for C. parvum. Transcriptomic analysis revealed changes in host immune response and metabolism, with increased abundance of type I interferon-responsive genes in STAg-treated C. parvum-infected mice. These findings contribute to the identification of future therapeutic targets for both host and parasite.
INFECTION AND IMMUNITY
(2022)
Article
Genetics & Heredity
Clifton P. Bueno de Mesquita, Jinglie Zhou, Susanna Theroux, Susannah G. Tringe
Summary: Aerobic bacteria that degrade methylphosphonates and produce methane have been found to play a crucial role in marine carbon and phosphorus cycles. In this study, two newly discovered species of the Marivita genus were identified from metagenomes of former industrial salterns with high salinity levels. These bacteria were found to be significantly more abundant in the salterns compared to nearby reference and restored wetlands.
Article
Multidisciplinary Sciences
Peicheng Sun, Xinxin Li, Adiphol Dilokpimol, Bernard Henrissat, Ronald P. de Vries, Mirjam A. Kabel, Miia R. Makela
Summary: This article introduces xyloglucanases (XEGs) and the GH44 family, which have been found in bacteria and fungi. Through genome analysis, GH44 enzymes from Dichomitus squalens and Pleurotus ostreatus were discovered and characterized. The study reveals that these fungal GH44 XEGs have different cleavage patterns during cellulose hydrolysis, indicating their potential for plant biomass conversion and utilization.
Article
Ecology
Mingsheng Qi, Jeffrey C. Berry, Kira W. Veley, Lily O'Connor, Omri M. Finkel, Isai Salas-Gonzalez, Molly Kuhs, Julietta Jupe, Emily Holcomb, Tijana Glavina del Rio, Cody Creech, Peng Liu, Susannah G. Tringe, Jeffery L. Dangl, Daniel P. Schachtman, Rebecca S. Bart
Summary: This study identified key root-associated microbial strains that significantly affect plant phenotypes under drought conditions in the staple cereal crop sorghum. The research found that certain Arthrobacter strains inhibit root growth, while Variovorax strains can protect plants from Arthrobacter-induced harm. The abundance of Arthrobacter was negatively correlated with plant growth in a field trial. By cross-referencing data from high-throughput phenotyping and field experiments, a list of bacteria positively associated with plant growth under drought stress was established.
Review
Microbiology
Clifton Bueno P. de Mesquita, Dongying Wu, Susannah G. Tringe
Summary: Methyl-based methanogenesis is one of the three broad categories of archaeal anaerobic methanogenesis, and it is recognized as an important source of methane in various environments.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Article
Multidisciplinary Sciences
Mia DeSanctis, Elizabeth M. Soranno, Ella Messner, Ziyu J. Wang, Elena L. Turner, Rosalia Falco, Hannah Appiah-Madson, Daniel Distel
Summary: EDTA is a chelator and preservative that can reduce DNA degradation in tissues by sequestering divalent cations. The effectiveness of EDTA as a DNA preservative can be improved by increasing its pH value. Our study showed that EDTA solutions with pH 10 preserved high molecular weight DNA better than tissues preserved in 95% ethanol.
Article
Biology
Marvin A. Altamia, Daniel L. Distel
Summary: Shipworms digest wood with cellulolytic enzymes supplied by symbiotic bacteria, which are located in a specialized tissue called Deshayes gland. The mechanism of enzyme transport from gill to gut in shipworms is not fully understood. In this study, a different mechanism of enzyme transport via the ducts of Deshayes was proposed and supported by immunohistochemical methods.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Justin P. Shaffer, Louis-Felix Nothias, Luke R. Thompson, Jon G. Sanders, Rodolfo A. Salido, Sneha P. Couvillion, Asker D. Brejnrod, Franck Lejzerowicz, Niina Haiminen, Shi Huang, Holly L. Lutz, Qiyun Zhu, Cameron Martino, James T. Morton, Smruthi Karthikeyan, Melissa Nothias-Esposito, Kai Duehrkop, Sebastian Boecker, Hyun Woo Kim, Alexander A. Aksenov, Wout Bittremieux, Jeremiah J. Minich, Clarisse Marotz, MacKenzie M. Bryant, Karenina Sanders, Tara Schwartz, Greg Humphrey, Yoshiki Vasquez-Baeza, Anupriya Tripathi, Laxmi Parida, Anna Paola Carrieri, Kristen L. Beck, Promi Das, Antonio Gonzalez, Daniel McDonald, Joshua Ladau, Soren M. Karst, Mads Albertsen, Gail Ackermann, Jeff DeReus, Torsten Thomas, Daniel Petras, Ashley Shade, James Stegen, Se Jin Song, Thomas O. Metz, Austin D. Swafford, Pieter C. Dorrestein, Janet K. Jansson, Jack A. Gilbert, Rob Knight
Summary: This study presents a multi-omics analysis framework for characterizing microbial communities across diverse habitats on Earth, demonstrating relationships between metabolites and microbial taxa and providing a reference database for future studies. The research showcases the significance of microbial and chemical ecology and lays a foundation for multi-omics microbiome studies.
NATURE MICROBIOLOGY
(2022)
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.
News Item
Microbiology
Rex R. Malmstrom
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Plant Sciences
Qing Zheng, Yuntao Hu, Suzanne M. Kosina, Marc W. Van Goethem, Susannah G. Tringe, Benjamin P. Bowen, Trent R. Northen
Summary: Biocrusts, phototroph-driven communities in arid soil, have beneficial interactions with cyanosphere bacteria similar to those in the rhizosphere. This study found that biocrust microbes promote the growth of a model grass and a dominant biocrust cyanobacterium, and identified specific strains that significantly promote the growth of both hosts. Furthermore, a metabolite produced by one of the strains increased the biomass of the model grass. These findings indicate that biocrusts and diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.
Article
Forestry
Antonio J. Fernandez-Gonzalez, Ana V. V. Lasa, Jose F. Cobo-Diaz, Pablo J. J. Villadas, Antonio J. J. Perez-Luque, Fernando M. M. Garcia-Rodriguez, Susannah G. G. Tringe, Manuel Fernandez-Lopez
Summary: The long-term recovery of prokaryotic communities in a Mediterranean ecosystem after a forest fire is not yet complete, even after a decade. Specific biomarkers, including the genera Arthrobacter, Blastococcus, and Massilia, persist in the soil microbial communities for an extended period of time.
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.