Article
Agricultural Engineering
Wenqian Zhao, Xiaodong Zhang, Yanpeng Cai, Shan Zhao, Shuguang Wang
Summary: MNZ inhibits anaerobic fermentation more strongly in mesophilic conditions than in thermophilic conditions. It can be completely removed through biodegradation. MNZ reduces the abundance of hydrogen-producing bacteria and its inhibition on anaerobic fermentation is reversible.
BIORESOURCE TECHNOLOGY
(2022)
Article
Engineering, Environmental
G. Cazaudehore, F. Monlau, C. Gassie, A. Lallement, R. Guyoneaud
Summary: This study investigates the treatment of biodegradable plastics under mesophilic and thermophilic anaerobic digestion and the microorganisms involved in the process. It is found that PHB and TPS can be rapidly degraded at mesophilic condition, while PCL and PLA have low degradation rates. At thermophilic conditions, TPS, PHB, and PLA can be effectively degraded, while PBS, PBAT, and PCL cannot be converted to methane. PHB degraders and lactate-utilizing bacteria play important roles in the degradation process.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
G. Cazaudehore, F. Monlau, C. Gassie, A. Lallement, R. Guyoneaud
Summary: The biodegradable plastics in coffee capsules were compared under mesophilic and thermophilic anaerobic digestion conditions, with the latter showing better degradation efficiency. Different biodegradable plastics had minimal impact on microbial community composition, with the genus Tepidimicrobium identified as a key microorganism involved in the thermophilic conversion of biodegradable plastic into methane.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Agricultural Engineering
Mark T. Holtzapple, Haoran Wu, Paul J. Weimer, Rachel Dalke, Cesar B. Granda, Jesse Mai, Meltem Urgun-Demirtas
Summary: The carboxylate platform utilizes a diverse microbial consortium to digest biomass and produce high yields of products without sterilization, accepting a wide range of feedstocks. It is highlighted for its thermodynamic basis, inoculum source and operating conditions, and downstream chemical processes for converting carboxylates to fuels and chemicals, establishing it as a viable and economical route for industrial biomass utilization.
BIORESOURCE TECHNOLOGY
(2022)
Article
Engineering, Environmental
Qinxue Wen, Shuo Yang, Zhiqiang Chen
Summary: The study found that sulfamethoxazole had a significant impact on the microbial community and resistance genes, while norfloxacin had little influence. Thermophilic anaerobic digestion showed higher methane production potential and greater reduction in resistance gene abundance.
FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING
(2021)
Article
Energy & Fuels
Mariana Murillo-Roos, Lorena Uribe-Lorio, Paola Fuentes-Schweizer, Daniela Vidaurre-Barahona, Laura Brenes-Guillen, Ivannia Jimenez, Tatiana Arguedas, Wei Liao, Lidieth Uribe
Summary: Biomass from agricultural operations in Costa Rica has potential as a renewable resource for bioenergy generation. This study found that increasing digestion temperature and adding food wastes can significantly enhance biogas production and methane content. The microbial community structure also differs between thermophilic and mesophilic digestion, with higher species richness in thermophilic digestions.
Article
Chemistry, Multidisciplinary
Bing Xu, Qiang Li, Yuanqiao Pu, Shangxian Xie, Arthur J. Ragauskas, Jorge Arreola-Vargas, Zhi-Hua Liu, Joshua S. Yuan
Summary: Pelletized liquid cultivation has advantages in biomanufacturing, and this study discovered that nonfilamentous bacterium Rhodococcus opacus PD630 can form pellets during fermentation. The study provides new insights into bacterium pelletization.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Environmental Sciences
Xiaohui Liu, Changmin Lee, Jae Young Kim
Summary: This study investigated the potential of thermophilic anaerobic digestion combined with thermal hydrolysis pretreatment for maximizing biogas yield from swine manure. The results showed that the combined treatment significantly increased methane production and ensured a sustainable digestion process with microbial diversity. Improving the energetic efficiency of the pretreatment units is crucial for the development of this treatment mode.
JOURNAL OF ENVIRONMENTAL SCIENCES
(2023)
Correction
Microbiology
Pankaj Trivedi, Jan E. Leach, Susannah G. Tringe, Tongmin Sa, Brajesh K. Singh
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Microbiology
Katelyn McNair, Carol L. Ecale Zhou, Brian Souza, Stephanie Malfatti, Robert A. Edwards
Summary: One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. Differentiating the actual protein-coding ORFs from random occurrences can be done using methods like shared homology comparison with known genes or using tools like GOODORFS which calculates amino acid frequencies, entropy density profiles, clusters the profiles, and selects coding ORFs with the lowest variation. Testing on annotated phage genomes showed GOODORFS to be the most accurate and have the best F1-score, while other methods like Glimmer had higher precision and PHANOTATE had higher recall.
Correction
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I- Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
NATURE BIOTECHNOLOGY
(2021)
Article
Ecology
Jinglie Zhou, Susanna M. Theroux, Clifton P. Bueno de Mesquita, Wyatt H. Hartman, Ye Tian, Susannah G. Tringe
Summary: The study showed that wetland restoration effectively restored microbial communities in former industrial salt ponds to compositions more similar to reference wetlands, reducing salinity, sulfate concentrations, and methane emissions.
Article
Biochemistry & Molecular Biology
Elle M. Barnes, Susannah G. Tringe
Summary: Plants benefit from their association with soil microbes in responding to stress, but much is unknown about these interactions. Climate change affects both plants and soil microbial communities, necessitating a multi-dimensional approach to studying their interactions. New tools, such as fabricated ecosystems and synthetic communities, can help researchers explore plant-microbe-environment interactions with more precision.
BIOCHEMICAL JOURNAL
(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
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.
News Item
Microbiology
Susannah G. Tringe
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Ecology
Naihao Ye, Wentao Han, Andrew Toseland, Yitao Wang, Xiao Fan, Dong Xu, Cock van Oosterhout, Igor Grigoriev, Alessandro Tagliabue, Jian Zhang, Yan Zhang, Jian Ma, Huan Qiu, Youxun Li, Xiaowen Zhang, Thomas Mock
Summary: This study reveals that polar microalgae have a higher demand for zinc due to elevated cellular levels of zinc-binding proteins. Zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton, which is critical for algal colonization of low-temperature polar oceans.
NATURE ECOLOGY & EVOLUTION
(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
Igor Brown, Tanja Woyke, Natalia Ivanova, Nicole Shapiro, Jaime Alcorta, Andrei Chistoserdov, Donald Pan, Svetlana Sarkisova, Susannah G. Tringe
Summary: The draft genome sequence of the siderophilic cyanobacterium Fischerella thermalis JSC-11, isolated from an iron-depositing hot spring, is reported. JSC-11 has bioremediation potential due to its ability to both extracellularly absorb and intracellularly mineralize colloidal iron. This genomic information will facilitate the exploration of JSC-11 for bioremediation.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
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
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
Environmental Sciences
Brett D. Van Houghton, Shwetha M. Acharya, James S. Rosenblum, Romy Chakraborty, Susannah Green Tringe, Tzahi Y. Cath
Summary: The study showed that membrane bioreactors (MBRs) exhibit excellent long-term performance in removing organic constituents from produced water (PW), even in high salinity conditions. MBRs were effective in removing dissolved organic carbon from PW from different shale basins, but showed less consistent removal of surfactants. The study also found that microbial diversity decreased during reactor establishment but increased at higher total dissolved solid (TDS) concentrations.