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Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming ISME J. (IF 11.0) Pub Date : 2024-05-09 Andrea Söllinger, Laureen S Ahlers, Mathilde Borg Dahl, Páll Sigurðsson, Coline Le Noir de Carlan, Biplabi Bhattarai, Christoph Gall, Victoria S Martin, Cornelia Rottensteiner, Liabo L Motleleng, Eva Marie Breines, Erik Verbruggen, Ivika Ostonen, Bjarni D Sigurdsson, Andreas Richter, Alexander T Tveit
Physiological responses of soil microorganisms to global warming are important for soil ecosystem function and the terrestrial carbon cycle. Here, we investigate the effects of weeks, years, and decades of soil warming across seasons and time on the microbial protein biosynthesis machineries (i.e. ribosomes), the most abundant cellular macromolecular complexes, using RNA:DNA and RNA:MBC (microbial
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Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures ISME J. (IF 11.0) Pub Date : 2024-05-08 Wei Li, David Baliu-Rodriguez, Sanduni H Premathilaka, Sharmila I Thenuwara, Jeffrey A Kimbrel, Ty J Samo, Christina Ramon, E Anders Kiledal, Sara R Rivera, Jenan Kharbush, Dragan Isailovic, Peter K Weber, Gregory J Dick, Xavier Mayali
Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs, and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments
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Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments ISME J. (IF 11.0) Pub Date : 2024-05-06 Jiulong Zhao, Shailesh Nair, Zenghu Zhang, Zengmeng Wang, Nianzhi Jiao, Yongyu Zhang
The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing
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Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria ISME J. (IF 11.0) Pub Date : 2024-05-06 Le Liu, Xiang Gao, Changjie Dong, Huanyu Wang, Xiaofeng Chen, Xiaoyi Ma, Shujing Liu, Quanrui Chen, Dan Lin, Nianzhi Jiao, Kai Tang
Chirality, a fundamental property of matter, is often overlooked in the studies of marine organic matter cycles. Dihydroxypropanesulfonate (DHPS), a globally abundant organosulfur compound, serves as an ecologically important currency for nutrient and energy transfer from phytoplankton to bacteria in the ocean. However, the chirality of DHPS in nature and its transformation remain unclear. Here, we
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Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction ISME J. (IF 11.0) Pub Date : 2024-05-01 Ingrid Richter, Mahmudul Hasan, Johannes W Kramer, Philipp Wein, Jana Krabbe, K Philip Woitas, Timothy P Stinear, Sacha J Pidot, Florian Kloss, Christian Hertweck, Gerald Lackner
The endosymbiosis between the pathogenic fungus Rhizopus microsporus and the toxin-producing bacterium Mycetohabitans rhizoxinica represents a unique example of host control by an endosymbiont. Fungal sporulation strictly depends on the presence of endosymbionts as well as bacterially produced secondary metabolites. However, an influence of primary metabolites on host control remained unexplored. Recently
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Depletion of protective microbiota promotes the incidence of fruit disease ISME J. (IF 11.0) Pub Date : 2024-05-01 Xue Luo, Kai Sun, Hao-Ran Li, Xiang-Yu Zhang, Yi-Tong Pan, De-Lin Luo, Yi-Bo Wu, Hui-Jun Jiang, Xiao-Han Wu, Chen-Yu Ma, Chuan-Chao Dai, Wei Zhang
Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data and microbiological culturable approaches, we reported that roots and fruits
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Distinct life cycle stages of an ectosymbiotic DPANN archaeon ISME J. (IF 11.0) Pub Date : 2024-05-01 Vasil A Gaisin, Marleen van Wolferen, Sonja-Verena Albers, Martin Pilhofer
DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell–cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic
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Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence ISME J. (IF 11.0) Pub Date : 2024-05-01 Etthel M Windels, Lloyd Cool, Eline Persy, Janne Swinnen, Paul Matthay, Bram Van den Bergh, Tom Wenseleers, Jan Michiels
Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known
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Mechanisms and implications of bacterial-fungal competition for soil resources ISME J. (IF 11.0) Pub Date : 2024-05-01 Chaoqun Wang, Yakov Kuzyakov
Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial
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Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism ISME J. (IF 11.0) Pub Date : 2024-05-01 Xianyi Xiong, Hans G Othmer, William R Harcombe
Antibiotic persistence (heterotolerance) allows a sub-population of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial
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Proton-pumping rhodopsins promote the growth and survival of phytoplankton in a highly variable ocean ISME J. (IF 11.0) Pub Date : 2024-04-30 William G Sunda, Adrian Marchetti
Proton-pumping rhodopsins (PPRs) utilize sunlight to produce cellular energy. They are widely distributed in marine phytoplankton and were recently shown to occur in the vacuolar membrane of a marine diatom, making the vacuole a second light transducing organelle. Of course, the first, the chloroplast, is where photosynthesis occurs. However, the two light-driven sources of cellular energy are quite
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Siderophores and competition for iron govern myxobacterial predation dynamics ISME J. (IF 11.0) Pub Date : 2024-04-29 Francisco Javier Contreras-Moreno, Aurelio Moraleda-Muñoz, Francisco Javier Marcos-Torres, Virginia Cuéllar, María José Soto, Juana Pérez, José Muñoz-Dorado
Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the
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Rhizobium determinants of rhizosphere persistence and root colonisation ISME J. (IF 11.0) Pub Date : 2024-04-26 Hayley E Knights, Vinoy K Ramachandran, Beatriz Jorrin, Raphael Ledermann, Jack D Parsons, Samuel T N Aroney, Philip S Poole
Bacterial persistence in the rhizosphere and colonisation of root niches are critical for the establishment of many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum and its host legumes. Despite this, most studies on R. leguminosarum have focused on its symbiotic lifestyle as an endosymbiont in root nodules. Here, we use random barcode transposon sequencing (RB-TnSeq)
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Bridging ecological assembly process and community stability upon bacterial invasions ISME J. (IF 11.0) Pub Date : 2024-04-25 Xipeng Liu, Joana Falcão Salles
Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli
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Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates ISME J. (IF 11.0) Pub Date : 2024-04-24 Sarah Shah, Katherine E Dougan, Yibi Chen, Rosalyn Lo, Gemma Laird, Michael D A Fortuin, Subash K Rai, Valentine Murigneux, Anthony J Bellantuono, Mauricio Rodriguez-Lanetty, Debashish Bhattacharya, Cheong Xin Chan
Dinoflagellates in the family Symbiodiniaceae are taxonomically diverse, predominantly symbiotic lineages that are well-known for their association with corals. The ancestor of these taxa is believed to have been free-living. The establishment of symbiosis (i.e., symbiogenesis) is hypothesised to have occurred multiple times during Symbiodiniaceae evolution, but its impact on genome evolution of these
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Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges ISME J. (IF 11.0) Pub Date : 2024-04-23 Bettina Glasl, Heidi M Luter, Katarina Damjanovic, Katharina Kitzinger, Anna J Mueller, Leonie Mahler, Joan Pamela Engelberts, Laura Rix, Jay T Osvatic, Bela Hausmann, Joana Séneca, Holger Daims, Petra Pjevac, Michael Wagner
Ammonia-oxidising archaea and nitrite-oxidising bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification - the aerobic oxidation of ammonia to nitrite and further to nitrate - and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterise two novel nitrifying symbiont
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Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates ISME J. (IF 11.0) Pub Date : 2024-04-22 Zoila I Alvarez-Aponte, Alekhya M Govindaraju, Zachary F Hallberg, Alexa M Nicolas, Myka A Green, Kenny C Mok, Citlali Fonseca-Garcia, Devin Coleman-Derr, Eoin L Brodie, Hans K Carlson, Michiko E Taga
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions
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Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments ISME J. (IF 11.0) Pub Date : 2024-04-22 Dilem Ruhluel, Lewis Fisher, Thomas E Barton, Hollie Leighton, Sumit Kumar, Paula Amores Morillo, Siobhan O’Brien, Joanne L Fothergill, Daniel R Neill
Pseudomonas aeruginosa is a cause of chronic respiratory tract infections in people with cystic fibrosis (CF), non-CF bronchiectasis and chronic obstructive pulmonary disease. Prolonged infection allows accumulation of mutations and horizontal gene transfer, increasing the likelihood of adaptive phenotypic traits. Adaptation is proposed to arise first in bacterial populations colonising upper airway
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Ecological relevance of flagellar motility in soil bacterial communities ISME J. (IF 11.0) Pub Date : 2024-04-22 Josep Ramoneda, Kunkun Fan, Jane M Lucas, Haiyan Chu, Andrew Bissett, Michael S Strickland, Noah Fierer
Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility
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Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont ISME J. (IF 11.0) Pub Date : 2024-04-18 Heidi Abresch, Tisza Bell, Scott R Miller
Many organisms have formed symbiotic relationships with nitrogen (N)-fixing bacteria to overcome N limitation. Diatoms in the family Rhopalodiaceae host unicellular, N-fixing cyanobacterial endosymbionts called spheroid bodies (SBs). Although this relationship is relatively young, SBs share many key features with older endosymbionts, including coordinated cell division and genome reduction. Unlike
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Anaerobic oxidation of ammonium and short-chain gaseous alkanes coupled to nitrate reduction by a bacterial consortium ISME J. (IF 11.0) Pub Date : 2024-04-16 Mengxiong Wu, Xiawei Liu, J Pamela Engelberts, Gene W Tyson, Simon J McIlroy, Jianhua Guo
The bacterial species ‘Candidatus Alkanivorans nitratireducens’ was recently demonstrated to mediate nitrate-dependent anaerobic oxidation of short-chain gaseous alkanes (SCGAs). In previous bioreactor enrichment studies1,2, the species appeared to reduce nitrate in two phases, switching from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) in response to nitrite accumulation.
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Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert ISME J. (IF 11.0) Pub Date : 2024-04-16 Zachary K Garvin, Sebastian R Abades, Nicole Trefault, Fernando D Alfaro, Katie Sipes, Karen G Lloyd, Tullis C Onstott
High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present “oases” of microbial activity, diversity, and abundance by delivering water and substrates, including reduced
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Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem ISME J. (IF 11.0) Pub Date : 2024-04-16 Delaney G Beals, Aaron W Puri
Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared to standard planktonic cultures, and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study
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Iron limitation of heterotrophic bacteria in the California current system tracks relative availability of organic carbon and iron ISME J. (IF 11.0) Pub Date : 2024-04-16 Lauren E Manck, Tyler H Coale, Brandon M Stephens, Kiefer O Forsch, Lihini I Aluwihare, Christopher L Dupont, Andrew E Allen, Katherine A Barbeau
Iron is an essential nutrient for all microorganisms in the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial
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Lactic acid bacteria modulate the CncC pathway to enhance resistance to β-cypermethrin in the oriental fruit fly ISME J. (IF 11.0) Pub Date : 2024-04-15 Tian Zeng, Qianyan Fu, Fangyi Luo, Jian Dai, Rong Fu, Yixiang Qi, Xiaojuan Deng, Yongyue Lu, Yijuan Xu
The gut microbiota of insects has been shown to regulate host detoxification enzymes. However, the potential regulatory mechanisms involved remain unknown. Here, we report that gut bacteria increase insecticide resistance by activating the cap “n” collar isoform-C (CncC) pathway through enzymatically generated reactive oxygen species (ROS) in Bactrocera dorsalis. We demonstrated that Enterococcus casseliflavus
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Soil redox status governs within-field spatial variation in microbial arsenic methylation and rice straighthead disease ISME J. (IF 11.0) Pub Date : 2024-04-02 A-Xiang Gao, Chuan Chen, Zi-Yu Gao, Zhi-Qiang Zhai, Peng Wang, Si-Yu Zhang, Fang-Jie Zhao
Microbial arsenic (As) methylation in paddy soil produces mainly dimethylarsenate (DMA), which can cause physiological straighthead disease in rice. The disease is often highly patchy in the field, but the reasons remain unknown. We investigated within-field spatial variations in straighthead disease severity, As species in rice husks and in soil porewater, microbial composition and abundance of arsM
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Dryland microbiomes reveal community adaptations to desertification and climate change ISME J. (IF 11.0) Pub Date : 2024-03-29 Claudia Coleine, Manuel Delgado-Baquerizo, Jocelyne DiRuggiero, Emilio Guirado, Antoine L Harfouche, Cesar Perez-Fernandez, Brajesh K Singh, Laura Selbmann, Eleonora Egidi
Drylands account for 45% of the Earth’s land area, supporting approximately 40% of the global population. These regions support some of the most extreme environments on Earth, characterized by extreme temperatures, low and variable rainfall, and low soil fertility. In these biomes, microorganisms provide vital ecosystem services and have evolved distinctive adaptation strategies to endure and flourish
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Environment-specific virocell metabolic reprogramming ISME J. (IF 11.0) Pub Date : 2024-03-29 Cristina Howard-Varona, Morgan M Lindback, Jane D Fudyma, Azriel Krongauz, Natalie E Solonenko, Ahmed A Zayed, William B Andreopoulos, Heather M Olson, Young-Mo Kim, Jennifer E Kyle, Tijana Glavina del Rio, Joshua N Adkins, Malak M Tfaily, Subhadeep Paul, Matthew B Sullivan, Melissa B Duhaime
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a “virocell”, is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that
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Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut ISME J. (IF 11.0) Pub Date : 2024-03-28 Yi Han Tan, Patricio Arros, Camilo Berríos-Pastén, Indrik Wijaya, Wilson H W Chu, Yahua Chen, Guoxiang Cheam, Ahmad Nazri Mohamed Naim, Andrés E Marcoleta, Aarthi Ravikrishnan, Niranjan Nagarajan, Rosalba Lagos, Yunn-Hwen Gan
The hypervirulent lineages of Klebsiella pneumoniae (HvKp) cause invasive infections such as Klebsiella-liver abscess. Invasive infection often occurs after initial colonisation of the host gastrointestinal tract by HvKp. Over 80% of HvKp isolates belong to the clonal group 23 sublineage I that has acquired genomic islands GIE492 and ICEKp10. Our analysis of 12,361 K. pneumoniae genomes revealed that
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Strategies for tailoring functional microbial synthetic communities ISME J. (IF 11.0) Pub Date : 2024-03-27 Jiayi Jing, Paolina Garbeva, Jos M Raaijmakers, Marnix H Medema
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial
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Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration ISME J. (IF 11.0) Pub Date : 2024-03-27 Yi-Tao Lin, Jack Chi-Ho Ip, Xing He, Zhao-Ming Gao, Maeva Perez, Ting Xu, Jin Sun, Pei-Yuan Qian, Jian-Wen Qiu
Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our
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Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change ISME J. (IF 11.0) Pub Date : 2024-03-21 Nathan S Garcia, Mingyu Du, Michele Guindani, Matt R McIlvin, Dawn M Moran, Mak A Saito, Adam C Martiny
Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature
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Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system ISME J. (IF 11.0) Pub Date : 2024-03-20 Kristin Barbour, Jennifer B H Martiny
Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter – topmost layer of surface soil – is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in southern California ecosystems. By leveraging a number of methodological
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Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion ISME J. (IF 11.0) Pub Date : 2024-03-19 Amelia R Nelson, Timothy S Fegel, Robert E Danczak, Marcos V Caiafa, Holly K Roth, Oliver I Dunn, Cosette A Turvold, Thomas Borch, Sydney I Glassman, Rebecca T Barnes, Charles C Rhoades, Michael J Wilkins
Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning – the combustion of logging residue on the forest floor – is a common fuel reduction practice that can have impacts on forest soils analogous to those following high severity wildfire. Further, pile burning following
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Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents ISME J. (IF 11.0) Pub Date : 2024-03-15 Raphael Gollnisch, Dag Ahrén, Karin Rengefors
The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears
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In vivo evolution of antimicrobial resistance in a biofilm model of Pseudomonas aeruginosa lung infection ISME J. (IF 11.0) Pub Date : 2024-03-13 Doaa Higazy, Anh Duc Pham, J G Coen van Hasselt, Niels Høiby, Lars Jelsbak, Claus Moser, Oana Ciofu
The evolution of antimicrobial resistance (AMR) in biofilms has been repeatedly studied by experimental evolution in vitro, but rarely in vivo. The complex microenvironment at the infection site imposes selective pressures on the bacterial biofilms, potentially influencing the development of AMR. We report here the development of AMR in an in vivo mouse model of Pseudomonas aeruginosa biofilm lung
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Niche differentiation in microbial communities with stable genomic traits over time in engineered systems ISME J. (IF 11.0) Pub Date : 2024-03-12 Jinjin Yu, Justin Y Y Lee, Siang Nee Tang, Patrick K H Lee
Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge (AS) and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models
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Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats ISME J. (IF 11.0) Pub Date : 2024-03-12 Paula C J Reis, Jackson M Tsuji, Cerrise Weiblen, Sherry L Schiff, Matthew Scott, Lisa Y Stein, Josh D Neufeld
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence on dioxygen (O2) for CH4 oxidation, abundant populations of putatively aerobic methanotrophs have been detected within microoxic and anoxic waters and sediments of
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Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action ISME J. (IF 11.0) Pub Date : 2024-03-11 Jan-Samuel Puls, Benjamin Winnerling, Jeffrey John Power, Annika Marie Krüger, Dominik Brajtenbach, Matthew Johnson, Kevser Bilici, Laura Camus, Thomas Fließwasser, Tanja Schneider, Hans-Georg Sahl, Debnath Ghosal, Ulrich Kubitscheck, Simon Heilbronner, Fabian Grein
Many bacteria produce antimicrobial compounds such as lantibiotics to gain advantage in the competitive natural environments of microbiomes. Epilancins constitute an until now underexplored family of lantibiotics with an unknown ecological role and unresolved mode of action. We discovered production of an epilancin in the nasal isolate Staphylococcus epidermidis A37. Using bioinformatic tools, we found
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SLC24A-mediated calcium exchange as an indispensable component of the diatom cell density-driven signaling pathway ISME J. (IF 11.0) Pub Date : 2024-03-08 Xuehua Liu, Zhicheng Zuo, Xiujun Xie, Shan Gao, Songcui Wu, Wenhui Gu, Guangce Wang
Diatom bloom is characterized by a rapid increase of population density. Perception of population density and physiological responses can significantly influence their survival strategies, subsequently impacting bloom fate. The population density itself can serve as a signal, which is perceived through chemical signals or chlorophyll fluorescence signals triggered by high cell density, and their intracellular
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Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs ISME J. (IF 11.0) Pub Date : 2024-03-07 Gordon Lax, Noriko Okamoto, Patrick J Keeling
Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they
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Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga ISME J. (IF 11.0) Pub Date : 2024-03-07 Nir Joffe, Constanze Kuhlisch, Guy Schleyer, Nadia Samira Ahlers, Adva Shemi, Assaf Vardi
Algal blooms drive global biogeochemical cycles of key nutrients and serve as hotspots for biological interactions in the ocean. The massive blooms of the cosmopolitan coccolithophore Emiliania huxleyi are often infected by the lytic E. huxleyi virus (EhV), which is a major mortality agent triggering bloom demise. This multi-annual “boom and bust” pattern of E. huxleyi blooms suggests that coexistence
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Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring ISME J. (IF 11.0) Pub Date : 2024-03-07 Mackenzie M Lynes, Zackary J Jay, Anthony J Kohtz, Roland Hatzenpichler
Over the past decade, environmental metagenomics and PCR-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic euryarchaeotes that have long been considered to live non-methanogenic lifestyles. Here
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Bacterial adenine cross-feeding stems from a purine salvage bottleneck ISME J. (IF 11.0) Pub Date : 2024-03-07 Ying-Chih Chuang, Nicholas W Haas, Robert Pepin, Megan G Behringer, Yasuhiro Oda, Breah LaSarre, Caroline S Harwood, James B McKinlay
Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we discovered purine externalization by Rhodopseudomonas palustris by its ability to rescue an Escherichia coli purine
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High niche specificity and host genetic diversity of groundwater viruses ISME J. (IF 11.0) Pub Date : 2024-03-06 Emilie Gios, Olivia E Mosley, Michael Hoggard, Kim M Handley
Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analyzed 16 metagenomes from a broad range of groundwater physicochemistries
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Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback ISME J. (IF 11.0) Pub Date : 2024-03-05 Yongchao Yin, Fadime Kara-Murdoch, Robert W Murdoch, Jun Yan, Gao Chen, Yongchao Xie, Yanchen Sun, Frank E Löffler
Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth
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Impact of airborne algicidal bacteria on marine phytoplankton blooms ISME J. (IF 11.0) Pub Date : 2024-03-05 Naama Lang-Yona, J Michel Flores, Tal Sharon Nir-Zadock, Inbal Nussbaum, Ilan Koren, Assaf Vardi
Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here
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Coordinated transcriptional response to environmental stress by a Synechococcus virus ISME J. (IF 11.0) Pub Date : 2024-03-03 Branko Rihtman, Alberto Torcello-Requena, Alevtina Mikhaylina, Richard J Puxty, Martha R J Clokie, Andrew D Millard, David J Scanlan
Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success. Phosphorus (P) is a major abiotic control on the marine cyanobacterium Synechococcus. Some viruses infecting Synechococcus have
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Gut microbiota facilitate adaptation of invasive moths to new host plants ISME J. (IF 11.0) Pub Date : 2024-02-27 Shouke Zhang, Feng Song, Jie Wang, Xiayu Li, Yuxin Zhang, Wenwu Zhou, Letian Xu
Gut microbiota are important in the adaptation of phytophagous insects to their plant hosts. However, the interaction between gut microbiomes and pioneering populations of invasive insects during their adaptation to new hosts, particularly in the initial phases of invasion, has been less studied. We studied the contribution of the gut microbiome to host adaptation in the globally recognized invasive
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Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals ISME J. (IF 11.0) Pub Date : 2024-02-27 Marcel Suleiman, Natalie Le Lay, Francesca Demaria, Boris A Kolvenbach, Mariana S Cretoiu, Owen L Petchey, Alexandre Jousset, Philippe F-X Corvini
Organic pollutants are an increasing threat for wildlife and humans. Managing their removal is however complicated by the difficulties in predicting degradation rates. In this work we demonstrate that the complexity of the pollutant profile, the set of co-existing contaminants, is a major driver of biodegradation in wastewater. We built representative assemblages out of one to five common pharmaceuticals
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Isolation of a widespread giant virus implicated in cryptophyte bloom collapse ISME J. (IF 11.0) Pub Date : 2024-02-22 Helena Henriques Vieira, Paul-Adrian Bulzu, Vojtěch Kasalicky, Markus Haber, Petr Znachor, Kasia Piwosz, Rohit Ghai
Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we
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Entomopathogenic pseudomonads can share an insect host with entomopathogenic nematodes and their mutualistic bacteria ISME J. (IF 11.0) Pub Date : 2024-02-19 Maria Zwyssig, Anna Spescha, Tabea Patt, Adrian Belosevic, Ricardo A R Machado, Alice Regaiolo, Christoph Keel, Monika Maurhofer
A promising strategy to overcome limitations in biological control of insect pests is the combined application of entomopathogenic pseudomonads (EPPs) and nematodes (EPNs) associated with mutualistic bacteria (NABs). Yet, little is known about interspecies interactions such as competition, coexistence, or even cooperation between these entomopathogens when they infect the same insect host. We investigated
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Stronger compensatory thermal adaptation of soil microbial respiration with higher substrate availability ISME J. (IF 11.0) Pub Date : 2024-02-12 Lingrui Qu, Chao Wang, Stefano Manzoni, Marina Dacal, Fernando T Maestre, Edith Bai
Ongoing global warming is expected to augment soil respiration by increasing microbial activity, driving self-reinforcing feedback to climate change. However, the compensatory thermal adaptation of soil microorganisms and substrate depletion may weaken the effects of rising temperature on soil respiration. To test this hypothesis, we collected soils along a large-scale forest transect in eastern China
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Transglobal spread of an ecologically relevant sea urchin parasite ISME J. (IF 11.0) Pub Date : 2024-02-08 Isabella T Ritchie, Brayan Vilanova-Cuevas, Ashley Altera, Kaileigh Cornfield, Ceri Evans, James S Evans, Maria Hopson-Fernandes, Christina A Kellogg, Elayne Looker, Oliver Taylor, Ian Hewson, Mya Breitbart
Mass mortality of the dominant coral reef herbivore Diadema antillarum in the Caribbean in the early 1980s led to a persistent phase shift from coral- to algal-dominated reefs. In 2022, a scuticociliate most closely related to Philaster apodigitiformis caused further mass mortality of D. antillarum across the Caribbean, leading to >95% mortality at affected sites. Mortality was also reported in the
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Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms ISME J. (IF 11.0) Pub Date : 2024-02-05 Mira D Liu, Yongle Du, Sara K Koupaei, Nicole R Kim, Monika S Fischer, Wenjun Zhang, Matthew F Traxler
Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. While it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several
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Commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota ISME J. (IF 11.0) Pub Date : 2024-02-02 Ana Popovic, Eric Yixiao Cao, Joanna Han, Nirvana Nursimulu, Eliza V C Alves-Ferreira, Kyle Burrows, Andrea Kennard, Noor Alsmadi, Michael E Grigg, Arthur Mortha, John Parkinson
Commensal protists and gut bacterial communities exhibit complex relationships, mediated at least in part through host immunity. To improve our understanding of this tripartite interplay, we investigated community and functional dynamics between the murine protist Tritrichomonas musculus (Tmu) and intestinal bacteria in healthy and B cell-deficient mice. We identified dramatic, protist-driven remodeling
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Selection of photosynthetic traits by turbulent mixing governs formation of cyanobacterial blooms in shallow eutrophic lakes ISME J. (IF 11.0) Pub Date : 2024-02-02 Huaming Wu, Xingqiang Wu, Lorenzo Rovelli, Andreas Lorke
Prediction of the complex cyanobacteria-environment interactions is vital for understanding harmful bloom formation. Most previous studies on these interactions considered specific properties of cyanobacterial cells as representative for the entire population (e.g., growth rate, mortality, and photosynthetic capacity (Pmax)), and assumed that they remained spatiotemporally unchanged. Although, at the
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Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens ISME J. (IF 11.0) Pub Date : 2024-02-01 Esther Rubio-Portillo, Sophia Robertson, Josefa Antón
The increasing trend in sea surface temperature promotes the spread of Vibrio species, which are known to cause diseases in a wide range of marine organisms. Among these pathogens, Vibrio mediterranei has emerged as a significant threat, leading to bleaching in the coral species Oculina patagonica. Bacteriophages, or phages, are viruses that infect bacteria, thereby regulating microbial communities
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Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments ISME J. (IF 11.0) Pub Date : 2024-02-01 Elias Broman, Markus Olsson, Adele Maciute, Daniel Donald, Christoph Humborg, Alf Norkko, Tom Jilbert, Stefano Bonaglia, Francisco J A Nascimento
Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial–temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment–water fluxes and aerobic methanotrophic activity that can oxidize
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Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth ISME J. (IF 11.0) Pub Date : 2024-01-29 Nan Yang, Henriette L Røder, Wisnu Adi Wicaksono, Birgit Wassermann, Jakob Russel, Xuanji Li, Joseph Nesme, Gabriele Berg, Søren J Sørensen, Mette Burmølle
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans and Xanthomonas