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Volume 19, Issue 1, January 2025
Perspective
Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus
The ISME Journal, Volume 19, Issue 1, January 2025, wraf011, https://doi.org/10.1093/ismejo/wraf011
Metabolic labour division trade-offs in denitrifying microbiomes
The ISME Journal, Volume 19, Issue 1, January 2025, wraf020, https://doi.org/10.1093/ismejo/wraf020
Review Articles
Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota
The ISME Journal, Volume 19, Issue 1, January 2025, wrae253, https://doi.org/10.1093/ismejo/wrae253
Emerging role of rare earth elements in biomolecular functions
The ISME Journal, Volume 19, Issue 1, January 2025, wrae241, https://doi.org/10.1093/ismejo/wrae241
Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum
The ISME Journal, Volume 19, Issue 1, January 2025, wraf023, https://doi.org/10.1093/ismejo/wraf023
Microbial ecology of serpentinite-hosted ecosystems
The ISME Journal, Volume 19, Issue 1, January 2025, wraf029, https://doi.org/10.1093/ismejo/wraf029
Ecological and evolutionary responses of earthworm holobionts to environmental changes
The ISME Journal, Volume 19, Issue 1, January 2025, wraf044, https://doi.org/10.1093/ismejo/wraf044
Metabolism of CO and H2 by pioneer bacteria in volcanic soils and the phyllosphere
The ISME Journal, Volume 19, Issue 1, January 2025, wraf053, https://doi.org/10.1093/ismejo/wraf053
Brief Communications
Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa
The ISME Journal, Volume 19, Issue 1, January 2025, wraf012, https://doi.org/10.1093/ismejo/wraf012
Phylogenomic resolution of marine to freshwater dinoflagellate transitions
The ISME Journal, Volume 19, Issue 1, January 2025, wraf031, https://doi.org/10.1093/ismejo/wraf031
Mice expressing the autism-associated neuroligin-3 R451C variant exhibit increased mucus density and altered distributions of intestinal microbiota
The ISME Journal, Volume 19, Issue 1, January 2025, wraf037, https://doi.org/10.1093/ismejo/wraf037
Original Articles
Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series
The ISME Journal, Volume 19, Issue 1, January 2025, wrae245, https://doi.org/10.1093/ismejo/wrae245
Two waves of photosymbiosis acquisition in extant planktonic foraminifera explained by ecological incumbency
The ISME Journal, Volume 19, Issue 1, January 2025, wrae244, https://doi.org/10.1093/ismejo/wrae244
Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments
The ISME Journal, Volume 19, Issue 1, January 2025, wrae248, https://doi.org/10.1093/ismejo/wrae248
Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment
The ISME Journal, Volume 19, Issue 1, January 2025, wrae252, https://doi.org/10.1093/ismejo/wrae252
Polymerization of dietary fructans differentially affects interactions among intestinal microbiota of colitis mice
The ISME Journal, Volume 19, Issue 1, January 2025, wrae262, https://doi.org/10.1093/ismejo/wrae262
Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture
The ISME Journal, Volume 19, Issue 1, January 2025, wrae259, https://doi.org/10.1093/ismejo/wrae259
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate
The ISME Journal, Volume 19, Issue 1, January 2025, wrae260, https://doi.org/10.1093/ismejo/wrae260
Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population
The ISME Journal, Volume 19, Issue 1, January 2025, wrae257, https://doi.org/10.1093/ismejo/wrae257
Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island
The ISME Journal, Volume 19, Issue 1, January 2025, wrae258, https://doi.org/10.1093/ismejo/wrae258
Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions
The ISME Journal, Volume 19, Issue 1, January 2025, wrae263, https://doi.org/10.1093/ismejo/wrae263
Dispersal promotes stability and persistence of exploited yeast mutualisms
The ISME Journal, Volume 19, Issue 1, January 2025, wraf003, https://doi.org/10.1093/ismejo/wraf003
Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments
The ISME Journal, Volume 19, Issue 1, January 2025, wraf004, https://doi.org/10.1093/ismejo/wraf004
Abundant and active community members respond to diel cycles in hot spring phototrophic mats
The ISME Journal, Volume 19, Issue 1, January 2025, wraf001, https://doi.org/10.1093/ismejo/wraf001
Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae
The ISME Journal, Volume 19, Issue 1, January 2025, wraf002, https://doi.org/10.1093/ismejo/wraf002
Long-term climate establishes functional legacies by altering microbial traits
The ISME Journal, Volume 19, Issue 1, January 2025, wraf005, https://doi.org/10.1093/ismejo/wraf005
Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut
The ISME Journal, Volume 19, Issue 1, January 2025, wraf016, https://doi.org/10.1093/ismejo/wraf016
Ecological histories govern social exploitation by microorganisms
The ISME Journal, Volume 19, Issue 1, January 2025, wrae255, https://doi.org/10.1093/ismejo/wrae255
Tolerance to land-use changes through natural modulations of the plant microbiome
The ISME Journal, Volume 19, Issue 1, January 2025, wraf010, https://doi.org/10.1093/ismejo/wraf010
Occurrence of “under-the-radar” antibiotic resistance in anthropogenically affected produce
The ISME Journal, Volume 19, Issue 1, January 2025, wrae261, https://doi.org/10.1093/ismejo/wrae261
Surfactin facilitates establishment of Bacillus subtilis in synthetic communities
The ISME Journal, Volume 19, Issue 1, January 2025, wraf013, https://doi.org/10.1093/ismejo/wraf013
Microbial competition for iron determines its availability to the ferrous wheel
The ISME Journal, Volume 19, Issue 1, January 2025, wraf015, https://doi.org/10.1093/ismejo/wraf015
Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota
The ISME Journal, Volume 19, Issue 1, January 2025, wraf017, https://doi.org/10.1093/ismejo/wraf017
Urea-based mutualistic transfer of nitrogen in biological soil crusts
The ISME Journal, Volume 19, Issue 1, January 2025, wrae246, https://doi.org/10.1093/ismejo/wrae246
Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance
The ISME Journal, Volume 19, Issue 1, January 2025, wraf009, https://doi.org/10.1093/ismejo/wraf009
Wide-ranging organic nitrogen diets of freshwater picocyanobacteria
The ISME Journal, Volume 19, Issue 1, January 2025, wrae236, https://doi.org/10.1093/ismejo/wrae236
Active bacteria driving N2O mitigation and dissimilatory nitrate reduction to ammonium in ammonia recovery bioreactors
The ISME Journal, Volume 19, Issue 1, January 2025, wraf021, https://doi.org/10.1093/ismejo/wraf021
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions
The ISME Journal, Volume 19, Issue 1, January 2025, wraf025, https://doi.org/10.1093/ismejo/wraf025
Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans
The ISME Journal, Volume 19, Issue 1, January 2025, wraf019, https://doi.org/10.1093/ismejo/wraf019
Genetic and species rearrangements in microbial consortia impact biodegradation potential
The ISME Journal, Volume 19, Issue 1, January 2025, wraf014, https://doi.org/10.1093/ismejo/wraf014
Metabolism of hemicelluloses by root-associated Bacteroidota species
The ISME Journal, Volume 19, Issue 1, January 2025, wraf022, https://doi.org/10.1093/ismejo/wraf022
Murine gut microbial interactions exert antihyperglycemic effects
The ISME Journal, Volume 19, Issue 1, January 2025, wraf028, https://doi.org/10.1093/ismejo/wraf028
Lysis of Escherichia coli by colicin Ib contributes to bacterial cross-feeding by releasing active β-galactosidase
The ISME Journal, Volume 19, Issue 1, January 2025, wraf032, https://doi.org/10.1093/ismejo/wraf032
Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment
The ISME Journal, Volume 19, Issue 1, January 2025, wraf042, https://doi.org/10.1093/ismejo/wraf042
Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks
The ISME Journal, Volume 19, Issue 1, January 2025, wraf027, https://doi.org/10.1093/ismejo/wraf027
Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction
The ISME Journal, Volume 19, Issue 1, January 2025, wraf033, https://doi.org/10.1093/ismejo/wraf033
Effects of microplastics on Daphnia-associated microbiomes in situ and in vitro
The ISME Journal, Volume 19, Issue 1, January 2025, wrae234, https://doi.org/10.1093/ismejo/wrae234
Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes
The ISME Journal, Volume 19, Issue 1, January 2025, wraf026, https://doi.org/10.1093/ismejo/wraf026
Carbon dioxide enhances Akkermansia muciniphila fitness and anti-obesity efficacy in high-fat diet mice
The ISME Journal, Volume 19, Issue 1, January 2025, wraf034, https://doi.org/10.1093/ismejo/wraf034
Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere
The ISME Journal, Volume 19, Issue 1, January 2025, wraf040, https://doi.org/10.1093/ismejo/wraf040
Strong segregation promotes self-destructive cooperation
The ISME Journal, Volume 19, Issue 1, January 2025, wraf043, https://doi.org/10.1093/ismejo/wraf043
Halophilic archaea produce wax esters and use an alternative fatty acyl-coenzyme A reductase for precursor synthesis
The ISME Journal, Volume 19, Issue 1, January 2025, wraf035, https://doi.org/10.1093/ismejo/wraf035
Spatio-temporal pattern formation of living organisms at the edge of chaos
The ISME Journal, Volume 19, Issue 1, January 2025, wraf050, https://doi.org/10.1093/ismejo/wraf050
Impact of micro-habitat fragmentation on microbial population growth dynamics
The ISME Journal, Volume 19, Issue 1, January 2025, wrae256, https://doi.org/10.1093/ismejo/wrae256
Microbiota contribute to regulation of the gut-testis axis in seasonal spermatogenesis
The ISME Journal, Volume 19, Issue 1, January 2025, wraf036, https://doi.org/10.1093/ismejo/wraf036
Metabolic interdependence and rewiring in radiolaria-microalgae photosymbioses
The ISME Journal, Volume 19, Issue 1, January 2025, wraf047, https://doi.org/10.1093/ismejo/wraf047
Interplay of ecological processes modulates microbial community reassembly following coalescence
The ISME Journal, Volume 19, Issue 1, January 2025, wraf041, https://doi.org/10.1093/ismejo/wraf041
Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification
The ISME Journal, Volume 19, Issue 1, January 2025, wraf054, https://doi.org/10.1093/ismejo/wraf054
Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice
The ISME Journal, Volume 19, Issue 1, January 2025, wrae250, https://doi.org/10.1093/ismejo/wrae250
Correlating phylogenetic and functional diversity of the nod-free but nodulating Bradyrhizobium phylogroup
The ISME Journal, Volume 19, Issue 1, January 2025, wraf030, https://doi.org/10.1093/ismejo/wraf030
Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate
The ISME Journal, Volume 19, Issue 1, January 2025, wraf046, https://doi.org/10.1093/ismejo/wraf046
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera
The ISME Journal, Volume 19, Issue 1, January 2025, wraf024, https://doi.org/10.1093/ismejo/wraf024
Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities
The ISME Journal, Volume 19, Issue 1, January 2025, wraf051, https://doi.org/10.1093/ismejo/wraf051
Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean
The ISME Journal, Volume 19, Issue 1, January 2025, wraf049, https://doi.org/10.1093/ismejo/wraf049
Bacillus subtilis ensures high spore quality in competition with Salmonella Typhimurium via the SigB-dependent pathway
The ISME Journal, Volume 19, Issue 1, January 2025, wraf052, https://doi.org/10.1093/ismejo/wraf052
Temperature influences outcomes of an environmentally acquired symbiosis
The ISME Journal, Volume 19, Issue 1, January 2025, wraf056, https://doi.org/10.1093/ismejo/wraf056
Extensive and diverse lanthanide-dependent metabolism in the ocean
The ISME Journal, Volume 19, Issue 1, January 2025, wraf057, https://doi.org/10.1093/ismejo/wraf057
Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction
The ISME Journal, Volume 19, Issue 1, January 2025, wraf064, https://doi.org/10.1093/ismejo/wraf064
Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants
The ISME Journal, Volume 19, Issue 1, January 2025, wraf058, https://doi.org/10.1093/ismejo/wraf058
Adaptive genomic plasticity in large-genome, broad-host–range vibrio phages
The ISME Journal, Volume 19, Issue 1, January 2025, wraf063, https://doi.org/10.1093/ismejo/wraf063
Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing
The ISME Journal, Volume 19, Issue 1, January 2025, wraf038, https://doi.org/10.1093/ismejo/wraf038
Corrections
Correction to 29 articles due to inaccurate manuscript submission dates
The ISME Journal, Volume 19, Issue 1, January 2025, wraf008, https://doi.org/10.1093/ismejo/wraf008
Correction to: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin
The ISME Journal, Volume 19, Issue 1, January 2025, wrae254, https://doi.org/10.1093/ismejo/wrae254
Correction to: Dryland microbiomes reveal community adaptations to desertification and climate change
The ISME Journal, Volume 19, Issue 1, January 2025, wraf060, https://doi.org/10.1093/ismejo/wraf060
