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Occurrence of “under-the-radar” antibiotic resistance in anthropogenically affected produce ISME J. (IF 10.8) Pub Date : 2025-02-06 Chagai Davidovich, Kseniia Erokhina, Chhedi Lal Gupta, Yong-Guan Zhu, Jian-Qiang Su, Steven P Djordjevic, Ethan R Wyrsch, Shlomo E Blum, Eddie Cytryn
With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen
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Active bacteria driving N2O mitigation and dissimilatory nitrate reduction to ammonium in ammonia recovery bioreactors ISME J. (IF 10.8) Pub Date : 2025-02-05 Hop V Phan, Shohei Yasuda, Kohei Oba, Hiroki Tsukamoto, Tomoyuki Hori, Megumi Kuroiwa, Akihiko Terada
Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge system for retaining ammonia whereas removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the system is essential to optimize system performance. Here, we employed metagenomics and metatranscriptomics
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Metabolism of hemicelluloses by root-associated Bacteroidota species ISME J. (IF 10.8) Pub Date : 2025-02-05 Hannah Martin, Lucy A Rogers, Laila Moushtaq, Amanda A Brindley, Polly Forbes, Amy R Quintion, Andrew R J Murphy, Helen Hipperson, Tim J Daniell, Didier Ndeh, Sam Amsbury, Andrew Hitchcock, Ian D E A Lidbury
Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species
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Metabolic labour division trade-offs in denitrifying microbiomes ISME J. (IF 10.8) Pub Date : 2025-02-04 Nina Roothans, Mark C M van Loosdrecht, Michele Laureni
Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification – the stepwise reduction of nitrate and nitrite to nitrogenous gases – is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies
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Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut ISME J. (IF 10.8) Pub Date : 2025-02-02 Chengfeng Yang, Benfeng Han, Junbo Tang, Jiawei Hu, Lifei Qiu, Wanzhi Cai, Xin Zhou, Xue Zhang
The maintenance of bacterial diversity at both species- and strain-levels is crucial for the sustainability of honey bee gut microbiota and host health. Periodic or random fluctuation in diet typically alters the metabolic niches available to gut microbes, thereby continuously reshaping bacterial diversity and interspecific interactions. It remains unclear how closely related bacteria adapt to these
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Microbial reaction rate estimation using proteins and proteomes ISME J. (IF 10.8) Pub Date : 2025-02-02 J Scott P McCain, Gregory L Britten, Sean R Hackett, Michael J Follows, Gene-Wei Li
Microbes transform their environments using diverse enzymatic reactions. However, it remains challenging to measure microbial reaction rates in natural environments. Despite advances in global quantification of enzyme abundances, the individual relationships between enzyme abundances and their reaction rates have not been systematically examined. Using matched proteomic and reaction rate data from
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Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota ISME J. (IF 10.8) Pub Date : 2025-02-02 Guido Zampieri, Davide Santinello, Matteo Palù, Esteban Orellana, Paola Costantini, Lorenzo Favaro, Stefano Campanaro, Laura Treu
Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised
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Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans ISME J. (IF 10.8) Pub Date : 2025-01-30 Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L Derie, Lindsey J du Toit, Stephen Stresow-Cortez, Jean M Bonasera, Paul Stodghill, Brian Kvitko
Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants
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Microbial competition for iron determines its availability to the ferrous wheel ISME J. (IF 10.8) Pub Date : 2025-01-27 Robert F Strzepek, Pauline Latour, Michael J Ellwood, Yeala Shaked, Philip W Boyd
Iron plays a pivotal role in regulating ocean primary productivity. Iron is supplied from diverse sources such as the atmosphere and the geosphere, and hence iron biogeochemical research has focused on identifying and quantifying such sources of “new” iron. However, the recycling of this new iron fuels up to 90% of the productivity in vast oceanic regions. Evidence points to the key role of microbes
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Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance ISME J. (IF 10.8) Pub Date : 2025-01-27 Chenshuo Lin, Li-Juan Li, Kai Yang, Jia-Yang Xu, Xiao-Ting Fan, Qing-Lin Chen, Yong-Guan Zhu
Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes. However, the effects of protozoan predation on antibiotic resistance genes dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse
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Genetic and species rearrangements in microbial consortia impact biodegradation potential ISME J. (IF 10.8) Pub Date : 2025-01-24 Zaki Saati-Santamaría, Pilar Navarro-Gómez, Juan A Martínez-Mancebo, Maitane Juárez-Mugarza, Amando Flores, Inés Canosa
Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants
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Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa ISME J. (IF 10.8) Pub Date : 2025-01-24 Ya Liu, Yu Geng, Yiru Jiang, Peng Li, Yue-zhong Li, Zheng Zhang
One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial
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Surfactin facilitates establishment of Bacillus subtilis in synthetic communities ISME J. (IF 10.8) Pub Date : 2025-01-22 Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács
Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many
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Tolerance to land-use changes through natural modulations of the plant microbiome ISME J. (IF 10.8) Pub Date : 2025-01-21 Vincent Zieschank, Anne Muola, Stefan Janssen, Alexander Lach, Robert R Junker
Land-use changes threaten ecosystems and are a major driver of species loss. Plants may adapt or migrate to resist global change, but this can lag behind rapid anthropogenic changes to the environment. Our data show that natural modulations of the microbiome of grassland plants in response to experimental land-use change in a common garden directly affect plant phenotype and performance, thus increasing
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Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus ISME J. (IF 10.8) Pub Date : 2025-01-21 Alexander B Alleman, Sergey Stolyar, Christopher J Marx, Jean-Baptiste Leducq
Although the 16S (and 18S) rRNA gene has been an essential tool in classifying prokaryotes, using a single locus to revise bacteria taxonomy can introduce unwanted artifacts. There was a recent proposition to split the Methylobacterium genus, which contains diverse plant-associated strains and is important for agriculture and biotechnology, into two genera. Resting strongly on the phylogeny of 16S
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Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments ISME J. (IF 10.8) Pub Date : 2025-01-20 Mathias Middelboe, Sachia J Traving, Daniel Castillo, Panos G Kalatzis, Ronnie N Glud
Auxiliary metabolic genes encoded by bacteriophages can influence host metabolic function during infection. In temperate phages, auxiliary metabolic genes may increase host fitness when integrated as prophages into the host genome. However, little is known about the contribution of prophage-encoded auxiliary metabolic genes to host metabolic properties. In this study, we examined a temperate bacteriophage
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Long-term climate establishes functional legacies by altering microbial traits ISME J. (IF 10.8) Pub Date : 2025-01-10 Caitlin M Broderick, Gian Maria Niccolò Benucci, Luciana Ruggiero Bachega, Gabriel D Miller, Sarah E Evans, Christine V Hawkes
Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence
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Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae ISME J. (IF 10.8) Pub Date : 2025-01-10 Sébastien Santini, Audrey Lartigue, Jean-Marie Alempic, Yohann Couté, Lucid Belmudes, William J Brazelton, Susan Q Lang, Jean-Michel Claverie, Matthieu Legendre, Chantal Abergel
The microbial sampling of submarine hydrothermal vents remains challenging, with even fewer studies focused on viruses. Here we report the first isolation of a eukaryotic virus from the Lost City hydrothermal field, by co-culture with the laboratory host Acanthamoeba castellanii. This virus, named pacmanvirus lostcity, is closely related to previously isolated pacmanviruses (strains A23 and S19), clustering
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Dispersal promotes stability and persistence of exploited yeast mutualisms ISME J. (IF 10.8) Pub Date : 2025-01-09 Cong Liu, Mayra C Vidal
Multi-species mutualistic interactions are ubiquitous and essential in nature, yet they face several threats, many of which have been exacerbated in the Anthropocene era. Understanding the factors that drive the stability and persistence of mutualism has become increasingly important in light of global change. Although dispersal is widely recognized as a crucial spatially explicit process in maintaining
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Abundant and active community members respond to diel cycles in hot spring phototrophic mats ISME J. (IF 10.8) Pub Date : 2025-01-08 Amanda N Shelton, Feiqiao B Yu, Arthur R Grossman, Devaki Bhaya
Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets
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Magnetotactic bacteria from diverse Pseudomonadota families biomineralize intracellular Ca-carbonate ISME J. (IF 10.8) Pub Date : 2025-01-07 Camille C Mangin, Karim Benzerara, Marine Bergot, Nicolas Menguy, Béatrice Alonso, Stéphanie Fouteau, Raphaël Méheust, Daniel Chevrier, Christian Godon, Elsa Turrini, Neha Mehta, Arnaud Duverger, Cynthia Travert, Vincent Busigny, Elodie Duprat, Romain Bolzoni, Corinne Cruaud, Eric Viollier, Didier Jézéquel, David Vallenet, Christopher T Lefèvre, Caroline L Monteil
Intracellular calcium carbonate formation has long been associated with a single genus of giant Gammaproteobacteria, Achromatium. However, this biomineralization has recently received increasing attention after being observed in photosynthetic Cyanobacteriota and in two families of magnetotactic bacteria affiliated with the Alphaproteobacteria. In the latter group, bacteria form not only intracellular
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Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions ISME J. (IF 10.8) Pub Date : 2025-01-03 Amanda M Zdimal, Giacomo Di Dio, Wanxiang Liu, Tanya Aftab, Taryn Collins, Remy Colin, Abhishek Shrivastava
The collective surface motility and swarming behavior of microbes play a crucial role in the formation of polymicrobial communities, shaping ecosystems as diverse as animal and human microbiota, plant rhizospheres, and various aquatic environments. In the human oral microbiota, T9SS-driven gliding bacteria transport non-motile microbes and bacteriophages as cargo, thereby influencing the spatial organization
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Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment ISME J. (IF 10.8) Pub Date : 2025-01-03 Sarah Bolius, Alexandra Schmidt, Jérôme Kaiser, Helge W Arz, Olaf Dellwig, Ulf Karsten, Laura S Epp, Anke Kremp
Dormancy is a wide-spread key life history trait observed across the tree of life. Many plankton species form dormant cells stages that accumulate in aquatic sediments and under anoxic conditions, form chronological records of past species and population dynamics under changing environmental conditions. Here we report on the germination of a microscopic alga, the abundant marine diatom Skeletonema
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Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the LEE pathogenicity island ISME J. (IF 10.8) Pub Date : 2025-01-02 Kat Pick, Lauren Stadel, Tracy L Raivio
In this study, we identify and characterize a novel phage-inducible chromosomal island found in commensal Escherichia coli MP1. This novel element, EcCIMP1, is induced and mobilized by the temperate helper phage vB_EcoP_Kapi1. EcCIMP1 contributes to superinfection immunity against its helper phage, impacting bacterial competition outcomes. Genetic analysis of EcCIMP1 led us to uncover a putative transcriptional
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Polymerization of dietary fructans differentially affects interactions among intestinal microbiota of colitis mice ISME J. (IF 10.8) Pub Date : 2025-01-02 Yaqin Xiao, Qianyun Zhao, Dawei Ni, Xiaoqi Zhang, Wei Hao, Qin Yuan, Wei Xu, Wanmeng Mu, Dingtao Wu, Xu Wu, Shengpeng Wang
The intestinal microbiota plays a critical role in maintaining human health and can be modulated by dietary interventions and lifestyle choices. Fructans, a dietary carbohydrate, are selectively utilized by the intestinal microbiota to confer health benefits. However, the specific effects of different fructan types on microbial changes and functions remain incompletely understood. Here, we investigated
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Ecological histories govern social exploitation by microorganisms ISME J. (IF 10.8) Pub Date : 2024-12-23 Kaitlin A Schaal, Pauline Manhes, Gregory J Velicer
Exploitation is a common feature of social interactions, which can be modified by ecological context. Here we investigate effects of ecological history on exploitation phenotypes in bacteria. In experiments with the bacterium Myxococcus xanthus, prior resource levels of different genotypes interacting during cooperative multicellular development were found to regulate social fitness, including whether
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Impact of micro-habitat fragmentation on microbial population growth dynamics ISME J. (IF 10.8) Pub Date : 2024-12-23 Dina Mant, Tomer Orevi, Nadav Kashtan
Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this
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Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population ISME J. (IF 10.8) Pub Date : 2024-12-23 Sotaro Takano, Miki Umetani, Hidenori Nakaoka, Ryo Miyazaki
Most of the microbes in nature infrequently receive nutrients and are thus in slow- or non-growing states. How quickly they can resume their growth upon an influx of new resources is crucial to occupy environmental niches. Isogenic microbial populations are known to harbor only a fraction of cells with rapid growth resumption, yet little is known about the physiological characteristics of those cells
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Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and co-culture ISME J. (IF 10.8) Pub Date : 2024-12-21 Zhiying Lu, Elizabeth Entwistle, Matthew D Kuhl, Alexander R Durrant, Marcelo Malisano Barreto Filho, Anuradha Goswami, J Jeffrey Morris
As a result of human activity, Earth’s atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here we experimentally evolved several phytoplankton in co-culture with
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Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota ISME J. (IF 10.8) Pub Date : 2024-12-18 Sophie-Carole Chobert, Morgane Roger-Margueritat, Laura Flandrin, Safa Berraies, Christopher T Lefèvre, Ludovic Pelosi, Ivan Junier, Nelle Varoquaux, Fabien Pierrel, Sophie S Abby
It is currently unclear how Pseudomonadota, a phylum that originated around the time of the Great Oxidation Event, became one of the most abundant and diverse bacterial phyla on Earth, with metabolically versatile members colonizing a wide range of environments with different O2 concentrations. Here, we address this question by studying isoprenoid quinones, which are central components of energy metabolism
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Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus ISME J. (IF 10.8) Pub Date : 2024-12-18 Eleanor C Arrington, Jonathan Tarn, Veronika Kivenson, Brook L Nunn, Rachel M Liu, Blair G Paul, David L Valentine
Aqueous-soluble hydrocarbons dissolve into the ocean’s interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning
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Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles ISME J. (IF 10.8) Pub Date : 2024-12-17 Qian Yang, Tom Defoirdt
Quorum sensing (QS) inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether QS inhibition will impose selective pressure for the spread of resistance against QS inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely
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Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice ISME J. (IF 10.8) Pub Date : 2024-12-16 Julianne C Yang, Venu Lagishetty, Ezinne Aja, Nerea Arias-Jayo, Candace Chang, Megan Hauer, William Katzka, Yi Zhou, Farzaneh Sedighian, Carolina Koletic, Fengting Liang, Tien S Dong, Jamilla Situ, Ryan Troutman, Heidi Buri, Shrikant Bhute, Carra A Simpson, Jonathan Braun, Noam Jacob, Jonathan P Jacobs
Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three
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Urea-based mutualistic transfer of nitrogen in biological soil crusts ISME J. (IF 10.8) Pub Date : 2024-12-14 Ana Mercedes Heredia-Velásquez, Soumyadev Sarkar, Finlay Warsop Thomas, Ariadna Cairó Baza, Ferran Garcia-Pichel
Foundational to establishment and recovery of biocrusts is a mutualistic exchange of carbon for nitrogen between pioneer cyanobacteria, including the widespread Microcoleus vaginatus, and heterotrophic diazotrophs in its “cyanosphere”. In other such mutualisms, nitrogen is transferred as amino acids or ammonium, preventing losses through specialized structures, cell apposition or intracellularity.
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Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments ISME J. (IF 10.8) Pub Date : 2024-12-13 Fatma Gomaa, Daniel R Rogers, Daniel R Utter, Christopher Powers, I-ting Huang, David J Beaudoin, Ying Zhang, Colleen Cavanaugh, Virginia P Edgcomb, Joan M Bernhard
Investigations of the metabolic capabilities of anaerobic protists advances our understanding of the evolution of eukaryotic life on Earth and for uncovering analogous extraterrestrial complex microbial life. Certain species of foraminiferan protists live in environments analogous to early Earth conditions when eukaryotes evolved, including sulfidic, anoxic, and hypoxic sediment porewaters. Foraminifera
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Effects of microplastics on daphnia-associated microbiomes in situ and in vitro ISME J. (IF 10.8) Pub Date : 2024-12-12 Anna Krzynowek, Broos Van de Moortel, Nikola Pichler, Isabel Vanoverberghe, Johanna Lapere, Liliana M Jenisch, Daphné Deloof, Wim Thielemans, Koenraad Muylaert, Michiel Dusselier, Dirk Springael, Karoline Faust, Ellen Decaestecker
Microplastic pollution in aquatic environments is a growing global concern. Microplastics, defined as plastic fragments smaller than five millimetres, accumulate in freshwater reservoirs, especially in urban areas, impacting resident biota. This study examined the effects of microplastics on the performance and microbiome of Daphnia, a keystone organism in freshwater ecosystems, through both in situ
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Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a twenty-year human gut time series ISME J. (IF 10.8) Pub Date : 2024-12-12 Bénédicte Condamine, Thibaut Morel-Journel, Florian Tesson, Guilhem Royer, Mélanie Magnan, Aude Bernheim, Erick Denamur, François Blanquart, Olivier Clermont
Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups
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Two waves of photosymbiosis acquisition in extant planktonic foraminifera explained by ecological incumbency ISME J. (IF 10.8) Pub Date : 2024-12-11 Haruka Takagi, Yasuhide Nakamura, Christiane Schmidt, Michal Kucera, Hiroaki Saito, Kazuyoshi Moriya
Photosymbiosis, a mode of mixotrophy by algal endosymbiosis, provides key advantage to pelagic life in oligotrophic oceans. Despite its ecological importance, mechanisms underlying its emergence and association with the evolutionary success of photosymbiotic lineages remain unclear. We used planktonic foraminifera, a group of pelagic test-forming protists with an excellent fossil record, to reveal
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Bilirubin reductase shows host-specific associations in animal large intestines ISME J. (IF 10.8) Pub Date : 2024-12-11 Keith Dufault-Thompson, Sophia Levy, Brantley Hall, Xiaofang Jiang
Animal gastrointestinal tracts contain diverse metabolites, including various host-derived compounds that gut-associated microbes interact with. Here, we explore the diversity and evolution of bilirubin reductase, a bacterial enzyme that metabolizes the host-derived tetrapyrrole bilirubin, performing a key role in the animal heme degradation pathway. Through an analysis of the bilirubin reductase phylogeny
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Transportome remodeling of a symbiotic microalga inside a planktonic host ISME J. (IF 10.8) Pub Date : 2024-12-11 Caroline Juéry, Adria Auladell, Zoltan Füssy, Fabien Chevalier, Daniel P Yee, Eric Pelletier, Erwan Corre, Andrew E Allen, Daniel J Richter, Johan Decelle
Metabolic exchange is one of the foundations of symbiotic associations between organisms and is a driving force in evolution. In the ocean, photosymbiosis between heterotrophic hosts and microalgae is powered by photosynthesis and relies on the transfer of organic carbon to the host (e.g. sugars). Yet, the identity of transferred carbohydrates as well as the molecular mechanisms that drive this exchange
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Bacteria of the order Burkholderiales are original environmental hosts of type II trimethoprim resistance genes (dfrB) ISME J. (IF 10.8) Pub Date : 2024-12-11 David Kneis, Faina Tskhay, Magali de la Cruz Barron, Thomas U Berendonk
It is consensus that clinically relevant antibiotic resistance genes have their origin in environmental bacteria, including the large pool of primarily benign species. Yet, for the vast majority of acquired antibiotic resistance genes, the original environmental host(s) has not been identified to date. Closing this knowledge gap could improve our understanding of how antimicrobial resistance proliferates
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Emerging role of rare earth elements in biomolecular functions ISME J. (IF 10.8) Pub Date : 2024-12-10 Wenyu Yang, Kaijuan Wu, Hao Chen, Jing Huang, Zheng Yu
The importance of rare earth elements is increasingly recognized due to the increased demand for their mining and separation. This demand is driving research on the biology of rare earth elements. Biomolecules associated with rare earth elements include rare earth element-dependent enzymes (methanol dehydrogenase XoxF, ethanol dehydrogenase ExaF/PedH), rare earth element-binding proteins, and the relevant
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Virophage infection mode determines ecological and evolutionary changes in a host-virus-virophage system ISME J. (IF 10.8) Pub Date : 2024-12-10 Ana del Arco, Lutz Becks
Giant viruses can control their eukaryotic host populations, shaping the ecology and evolution of aquatic microbial communities. Understanding the impact of the viruses’ own parasites, the virophages, on the control of microbial communities remains a challenge. Most virophages have two modes of infection. They can exist as free particles coinfecting host cells together with the virus, where they replicate
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Host-specific viral predation network on coral reefs ISME J. (IF 10.8) Pub Date : 2024-12-10 Natascha S Varona, Poppy J Hesketh-Best, Felipe H Coutinho, Alexandra K Stiffler, Bailey A Wallace, Sofia L Garcia, Yun Scholten, Andreas F Haas, Mark Little, Mark Vermeij, Antoni Luque, Cynthia Silveira
Viral infections are major modulators of marine microbial community assembly and biogeochemical cycling. In coral reefs, viral lysis controls bacterial overgrowth that is detrimental to coral health. However, methodological limitations have prevented the identification of viral hosts and quantification of their interaction frequencies. Here, we reconstructed an abundance-resolved virus–bacteria interaction
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Spatial sensing as a strategy for public goods regulation by gut microbes. ISME J. (IF 10.8) Pub Date : 2024-11-26 I Hashem,A Zhang,J Van Impe
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Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains ISME J. (IF 10.8) Pub Date : 2024-11-23 María Dolores Ramos-Barbero, Borja Aldeguer-Riquelme, Tomeu Viver, Judith Villamor, Miryam Carrillo-Bautista, Cristina López-Pascual, Konstantinos T Konstantinidis, Manuel Martínez-García, Fernando Santos, Ramon Rossello-Mora, Josefa Antón
Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background
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Trophic modulation of endophytes by rhizosphere protists ISME J. (IF 10.8) Pub Date : 2024-11-20 Rasit Asiloglu, Seda Ozer Bodur, Solomon Oloruntoba Samuel, Murat Aycan, Jun Murase, Naoki Harada
The plant-microbe interactions, which is crucial for plant health and productivity, mainly occur in rhizosphere: a narrow zone of soil surrounding roots of living plants. The rhizosphere hosts one of the most intense habitats for microbial prey–predator interactions, especially between predatory protists and bacteria. Here, based on two key facts, microbial predators modulate rhizobacterial community
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Coastal bacteria and protists assimilate viral carbon and nitrogen ISME J. (IF 10.8) Pub Date : 2024-11-13 Joaquín Martínez Martínez, David Talmy, Jeffrey A Kimbrel, Peter K Weber, Xavier Mayali
Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements
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Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules–gut countercurrent flow in Bactrocera dorsalis ISME J. (IF 10.8) Pub Date : 2024-11-12 Yanning Liu, Rengang Luo, Shuai Bai, Bruno Lemaitre, Hongyu Zhang, Xiaoxue Li
Host–gut microbiota interactions are more complex than good or bad. Both gut symbiotic bacteria and pathobionts can provide essential functions to their host in one scenario and yet be detrimental to host health in another. So, these gut-dwelling bacteria must be tightly controlled to avoid harmful effects on the host. However, how pathobionts and other symbiotic bacteria coordinate to establish a
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Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean ISME J. (IF 10.8) Pub Date : 2024-11-12 Nestor Arandia-Gorostidi, Alexander L Jaffe, Alma E Parada, Bennett J Kapili, Karen L Casciotti, Rebecca S R Salcedo, Chloé M J Baumas, Anne E Dekas
Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary
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Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria ISME J. (IF 10.8) Pub Date : 2024-11-09 Oscar Ramfelt, Kelle C Freel, Sarah J Tucker, Olivia D Nigro, Michael S Rappé
SAR86 is one of the most abundant groups of bacteria in the global surface ocean. However, since its discovery over 30 years ago, it has remained recalcitrant to isolation and many details regarding this group are still unknown. Here, we report the cellular characteristics from the first SAR86 isolate brought into culture, Magnimaribacter mokuoloeensis strain HIMB1674, and use its closed genome in
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Microbiome science of human excrement composting ISME J. (IF 10.8) Pub Date : 2024-11-09 Jeff Meilander, J Gregory Caporaso
Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of human excrement (human feces and urine) stands as a significant concern. Over two billion people do not have access to adequate sanitation, signifying a global public
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Aminolipids in bacterial membranes and the natural environment ISME J. (IF 10.8) Pub Date : 2024-11-09 Shengwei Liu, Eleonora Silvano, Mingyu Li, Michaela Mausz, Branko Rihtman, Richard Guillonneau, Otto Geiger, David J Scanlan, Yin Chen
Our comprehension of membrane function has predominantly advanced through research on glycerophospholipids, also known as phosphoglycerides, which are glycerol phosphate-based lipids found across all three domains of life. However, in bacteria, a perplexing group of lipids distinct from glycerol phosphate-based ones also exists. These are amino acid-containing lipids that form an amide bond between
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Biotics and bacterial function: impact on gut and host health ISME J. (IF 10.8) Pub Date : 2024-11-05 Anwar Kandari, Ma’en Al Odat, Fawaz Alzaid, Karen P Scott
The human gut microbiota, the vast community of microbes inhabiting the gastrointestinal tract, plays a pivotal role in maintaining health. Bacteria are the most abundant organism, and the composition of bacterial communities is strongly influenced by diet. Gut bacteria can degrade complex dietary carbohydrates to produce bioactive compounds such as short-chain fatty acids. Such products influence
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Sheaths are diverse and abundant cell surface layers in archaea ISME J. (IF 10.8) Pub Date : 2024-11-05 Sofia Medvedeva, Guillaume Borrel, Simonetta Gribaldo
Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings
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Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea ISME J. (IF 10.8) Pub Date : 2024-11-05 Hinako Takamiya, Mariko Kouduka, Shingo Kato, Hiroki Suga, Masaki Oura, Tadashi Yokoyama, Michio Suzuki, Masaru Mori, Akio Kanai, Yohey Suzuki
Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts
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Impact of timing on the invasion of synthetic bacterial communities ISME J. (IF 10.8) Pub Date : 2024-11-05 Keven D Dooley, Lucas P Henry, Joy Bergelson
Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process
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Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition ISME J. (IF 10.8) Pub Date : 2024-11-04 Ashish A Malik, Jennifer B H Martiny, Antonio Ribeiro, Paul O Sheridan, Claudia Weihe, Eoin L Brodie, Steven D Allison
Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates
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Probiotic model for studying rhizosphere interactions of root exudates and the functional microbiome ISME J. (IF 10.8) Pub Date : 2024-11-04 Zhiqiang Pang, Peng Xu
Root exudates are important mediators of plant–microbiome interactions. Recent pioneering studies on various aerial root plants, including cereals, have shown that carbohydrate-rich mucilage can enrich diazotrophs and increase host nitrogen utilization and growth. Moreover, non-diazotrophic “gatekeeper” microorganisms in mucilage help defend against pathogenic and environmental microbes. These findings
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Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities ISME J. (IF 10.8) Pub Date : 2024-11-03 Karl Alex Hedin, Mohammad H Mirhakkak, Troels Holger Vaaben, Carmen Sands, Mikael Pedersen, Adam Baker, Ruben Vazquez-Uribe, Sascha Schäuble, Gianni Panagiotou, Anja Wellejus, Morten Otto Alexander Sommer
Metabolic exchanges between strains in gut microbial communities shape their composition and interactions with the host. This study investigates the metabolic synergy between potential probiotic bacteria and Saccharomyces boulardii, aiming to enhance anti-inflammatory effects within a multi-species probiotic community. By screening a collection of 85 potential probiotic bacterial strains, we identified