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Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Oligopeptides Represent a Preferred Source of Organic N Uptake: A Global Phenomenon?
inferredcites →https://doi.org/10.1007/s11104-010-0387-1openalex-snapshot
Amino acid fingerprint of a grassland soil reflects changes in plant species richness
inferredcites →https://doi.org/10.1016/j.soilbio.2011.03.012openalex-snapshot
The under-recognized dominance of Verrucomicrobia in soil bacterial communities
inferredcites →https://doi.org/10.1016/s0038-0717(01)00185-7openalex-snapshot
Composition of hydrolysable amino acids in soil organic matter and soil microbial biomass
inferredcites →https://doi.org/10.1038/ismej.2012.122openalex-snapshot
Nutrient requirements for growth of the extreme oligotroph ‘ Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium
inferredcites →https://doi.org/10.1038/ismej.2014.60openalex-snapshot
Implications of streamlining theory for microbial ecology
inferredcites →https://doi.org/10.1038/ismej.2014.61openalex-snapshot
Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea
inferredcites →https://doi.org/10.1038/ismej.2015.54openalex-snapshot
Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils
inferredcites →https://doi.org/10.1038/ismej.2015.81openalex-snapshot
Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center
inferredcites →https://doi.org/10.1038/nature06411openalex-snapshot
Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.2openalex-snapshot
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
inferredcites →https://doi.org/10.1038/nrmicro3331openalex-snapshot
Reductive genome evolution at both ends of the bacterial population size spectrum
inferredcites →https://doi.org/10.1046/j.1472-765x.1998.00322.xopenalex-snapshot
Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils
inferredcites →https://doi.org/10.1073/pnas.0308653100openalex-snapshot
Trends between gene content and genome size in prokaryotic species with larger genomes
inferredcites →https://doi.org/10.1073/pnas.062526999openalex-snapshot
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
inferredcites →https://doi.org/10.1073/pnas.1215210110openalex-snapshot
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
inferredcites →https://doi.org/10.1073/pnas.1219451110openalex-snapshot
Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
inferredcites →https://doi.org/10.1073/pnas.1402564111openalex-snapshot
Tackling soil diversity with the assembly of large, complex metagenomes
inferredcites →https://doi.org/10.1073/pnas.1405641111openalex-snapshot
Syntrophic exchange in synthetic microbial communities
inferredcites →https://doi.org/10.1073/pnas.1508382112openalex-snapshot
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
inferredcites →https://doi.org/10.1093/bioinformatics/btm098openalex-snapshot
UniRef: comprehensive and non-redundant UniProt reference clusters
inferredcites →https://doi.org/10.1093/bioinformatics/btp636openalex-snapshot
PyNAST: a flexible tool for aligning sequences to a template alignment
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
inferredcites →https://doi.org/10.1093/gbe/evt050openalex-snapshot
Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation
inferredcites →https://doi.org/10.1093/nar/gkt963openalex-snapshot
IMG 4 version of the integrated microbial genomes comparative analysis system
inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot
The Pfam protein families database: towards a more sustainable future
inferredcites →https://doi.org/10.1093/nar/gkv657openalex-snapshot
Microbial species delineation using whole genome sequences
inferredcites →https://doi.org/10.1098/rspb.2014.1988openalex-snapshot
Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally
inferredcites →https://doi.org/10.1099/00207713-50-6-2197openalex-snapshot
Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae).
inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
inferredcites →https://doi.org/10.1111/1574-6976.12023openalex-snapshot
Micro-scale determinants of bacterial diversity in soil
inferredcites →https://doi.org/10.1111/1755-0998.12399openalex-snapshot
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
inferredcites →https://doi.org/10.1111/ele.12282openalex-snapshot
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
inferredcites →https://doi.org/10.1111/evo.12468openalex-snapshot
LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA
inferredcites →https://doi.org/10.1111/gcb.12565openalex-snapshot
Predicting the responsiveness of soil biodiversity to deforestation: a cross‐biome study
inferredcites →https://doi.org/10.1111/j.1461-0248.2009.01360.xopenalex-snapshot
Global patterns in belowground communities
inferredcites →https://doi.org/10.1111/mec.13319openalex-snapshot
Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community
inferredcites →https://doi.org/10.1126/science.1123061openalex-snapshot
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
inferredcites →https://doi.org/10.1126/science.1198078openalex-snapshot
Seasonality in Ocean Microbial Communities
inferredcites →https://doi.org/10.1126/science.1243768openalex-snapshot
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
inferredcites →https://doi.org/10.1128/aem.00429-08openalex-snapshot
Increased Fitness of Pseudomonas fluorescens Pf0-1 Leucine Auxotrophs in Soil
inferredcites →https://doi.org/10.1128/aem.02710-13openalex-snapshot
Cell Size Distributions of Soil Bacterial and Archaeal Taxa
inferredcites →https://doi.org/10.1128/aem.02772-15openalex-snapshot
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1128/aem.67.4.1636-1645.2001openalex-snapshot
Determination of DNA Content of Aquatic Bacteria by Flow Cytometry
inferredcites →https://doi.org/10.1128/aem.70.10.5875-5881.2004openalex-snapshot
Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia
inferredcites →https://doi.org/10.1128/aem.72.3.1719-1728.2006openalex-snapshot
Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes
inferredcites →https://doi.org/10.1128/br.22.3.145-153.1958openalex-snapshot
SOIL BACTERIA AND GROWTH-PROMOTING SUBSTANCES
inferredcites →https://doi.org/10.1128/genomea.00060-15openalex-snapshot
Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes
inferredcites →https://doi.org/10.1128/jb.00295-11openalex-snapshot
Genome Sequence of Chthoniobacter flavus Ellin428, an Aerobic Heterotrophic Soil Bacterium
inferredcites →https://doi.org/10.1128/mbio.00036-12openalex-snapshot
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
inferredcites →https://doi.org/10.1128/mbio.00569-12openalex-snapshot
Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria
inferredcites →https://doi.org/10.1128/mbio.00708-13openalex-snapshot
Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
inferredcites →https://doi.org/10.1186/1745-6150-3-26openalex-snapshot
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
inferredcites →https://doi.org/10.1186/gb-2007-8-1-r10openalex-snapshot
Prediction of effective genome size in metagenomic samples
inferredcites →https://doi.org/10.1186/gb-2009-10-8-r85openalex-snapshot
Community-wide analysis of microbial genome sequence signatures
inferredcites →https://doi.org/10.1186/gb-2011-12-5-r44openalex-snapshot
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
inferredcites →https://doi.org/10.1186/s13059-015-0611-7openalex-snapshot
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
inferredcites →https://doi.org/10.1371/journal.pone.0056018openalex-snapshot
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments
inferredcites →https://doi.org/10.15252/embj.201387076openalex-snapshot
Survival of mycobacteria depends on proteasome‐mediated amino acid recycling under nutrient limitation
inferredcites →https://doi.org/10.3389/fmicb.2012.00345openalex-snapshot
Genomic and Physiological Analysis of Carbon Storage in the Verrucomicrobial Methanotroph “Ca. Methylacidiphilum Fumariolicum” SolV
inferredcites →https://doi.org/10.3389/fmicb.2014.00750openalex-snapshot
Current strategies for mobilome research
inferredcites →https://doi.org/10.3732/ajb.1000498openalex-snapshot
The generation and maintenance of diversity in microbial communities
inferredcites →https://doi.org/10.7717/peerj.1029openalex-snapshot
Compact graphical representation of phylogenetic data and metadata with GraPhlAn

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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T errimicrobium
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inferred← citeshttps://doi.org/10.1002/mbo3.850openalex-snapshot
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Biodiversity, Microbiomes, and Human Health
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Role of Endophyte Metabolites in Plant Protection and Other Metabolic Activities
inferred← citeshttps://doi.org/10.1007/978-981-16-8918-5_6openalex-snapshot
Soil Verrucomicrobia and Their Role in Sustainable Agriculture
inferred← citeshttps://doi.org/10.1007/s00248-017-1129-1openalex-snapshot
Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra “Soils” of the Puna de Atacama Volcanic Zone
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Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient
inferred← citeshttps://doi.org/10.1007/s00248-022-02119-0openalex-snapshot
The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects
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Dirammox-dominated microbial community for biological nitrogen removal from wastewater
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Impact of Inoculation with Pseudomonas aestus CMAA 1215T on the Non-target Resident Bacterial Community in a Saline Rhizosphere Soil
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DNA Metabarcoding from Microbial Communities Recovered from Stream and Its Potential for Bioremediation Processes
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Network Analysis of Wheat and Couchgrass Rhizobacteria Highlights Candidate Biocontrol Agents for Improved Crop Resilience
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Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems
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Effects of quicklime application rate on carbon mineralization in strongly acidic soil of Chinese fir (Cunninghamia lanceolata) plantations
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Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia
inferred← citeshttps://doi.org/10.1007/s11274-021-03210-3openalex-snapshot
Total nitrogen influence bacterial community structure of active layer permafrost across summer and winter seasons in Ny-Ålesund, Svalbard
inferred← citeshttps://doi.org/10.1007/s11356-020-11290-1openalex-snapshot
Response of soil bacterial communities to high petroleum content in the absence of remediation procedures
inferred← citeshttps://doi.org/10.1007/s11356-025-35987-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11368-017-1680-xopenalex-snapshot
Verrucomicrobial elevational distribution was strongly influenced by soil pH and carbon/nitrogen ratio
inferred← citeshttps://doi.org/10.1007/s11427-020-1843-6openalex-snapshot
The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities
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Rhizocompartments and environmental factors affect microbial composition and variation in native plants
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Increased soil salinization slows biochar aging and limits microbial colonization
inferred← citeshttps://doi.org/10.1007/s42832-026-0481-9openalex-snapshot
Long-term organic fertilization fosters modular microbial networks: A global analysis of soil bacteriome responses
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20772-3openalex-snapshot
Phylum Verrucomicrobia
inferred← citeshttps://doi.org/10.1016/b978-0-12-819978-7.00015-4openalex-snapshot
Microbial Communities in Soils Under Natural Reforestation
inferred← citeshttps://doi.org/10.1016/b978-0-12-822941-5.00003-xopenalex-snapshot
Soil bacteria and archaea
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The relevant role of soil microorganisms in ameliorating abiotic stress in crop plants
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Early plant community changes in degraded alpine grasslands associated with restoration-induced shifts in soil and microbial communities on the Qinghai–Tibet Plateau
inferred← citeshttps://doi.org/10.1016/j.apsoil.2017.07.008openalex-snapshot
Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient
inferred← citeshttps://doi.org/10.1016/j.apsoil.2017.11.028openalex-snapshot
Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape
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Distribution of prokaryotic communities throughout the Chernozem profiles under different land uses for over a century
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Bacterial community associated with rhizosphere of maize and cowpea in a subsequent cultivation
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DNA stable isotope probing reveals a metabolic division of labour in haloalkaline oxalate-degrading bioreactors
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Effects of the polyhalogenated carbazoles 3-bromocarbazole and 1,3,6,8-tetrabromocarbazole on soil microbial communities
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Rebuilding microbiomes: Facilitating animal-microbe interactions through ecological restoration and rewilding
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Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress
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The diversity, composition and functions of soil bacterial communities surrounding Syowa Station, East Antarctica, under different intensities of human disturbances
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The complex interactions between novel DEHP-metabolising bacteria and the microbes in agricultural soils
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Impacts of snow-farming on alpine soil and vegetation: A case study from the Swiss Alps
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Biochar dose-dependent impacts on soil bacterial and fungal diversity across the globe
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Topography- and depth-dependent rhizosphere microbial community characteristics drive ecosystem multifunctionality in Juglans mandshurica forest
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Defoliation intensity and elevated precipitation effects on microbiome and interactome depend on site type in northern mixed-grass prairie
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Microtopographic differences in soil properties and microbial community composition at the field scale
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Bacterial communities of soil and earthworm casts of native Palouse Prairie remnants and no-till wheat cropping systems
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Linking soil microbial community structure to potential carbon mineralization: A continental scale assessment of reduced tillage
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Edaphic controls on genome size and GC content of bacteria in soil microbial communities
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Fertilization with microalgal biomass of wastewater treatment high-rate algae ponds (HRAP): Effects on the wheat root microbiome
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Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction
inferred← citeshttps://doi.org/10.1016/j.wateco.2025.100004openalex-snapshot
Adjustable microbial cross-feedings adapt to landforms in the Yangtze River
inferred← citeshttps://doi.org/10.1016/s1002-0160(21)60062-0openalex-snapshot
Difficult-to-culture bacteria in the rhizosphere: The underexplored signature microbial groups
inferred← citeshttps://doi.org/10.1029/2023jg007408openalex-snapshot
Comparing Sediment Microbial Communities of Arctic Beaver Ponds to Tundra Lakes and Streams
inferred← citeshttps://doi.org/10.1038/nrmicro.2016.174openalex-snapshot
A small soil bacterium dominates
inferred← citeshttps://doi.org/10.1038/nrmicro.2017.87openalex-snapshot
Embracing the unknown: disentangling the complexities of the soil microbiome
inferred← citeshttps://doi.org/10.1038/s41396-018-0232-8openalex-snapshot
Genetic correlation network prediction of forest soil microbial functional organization
inferred← citeshttps://doi.org/10.1038/s41396-019-0552-3openalex-snapshot
Unlinked rRNA genes are widespread among bacteria and archaea
inferred← citeshttps://doi.org/10.1038/s41396-020-00834-5openalex-snapshot
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning
inferred← citeshttps://doi.org/10.1038/s41396-021-01082-xopenalex-snapshot
Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria
inferred← citeshttps://doi.org/10.1038/s41467-018-05516-7openalex-snapshot
Soil bacterial networks are less stable under drought than fungal networks
inferred← citeshttps://doi.org/10.1038/s41467-023-43435-4openalex-snapshot
Taxonomic and environmental distribution of bacterial amino acid auxotrophies
inferred← citeshttps://doi.org/10.1038/s41522-024-00583-9openalex-snapshot
DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon
inferred← citeshttps://doi.org/10.1038/s41559-023-02027-7openalex-snapshot
A social niche breadth score reveals niche range strategies of generalists and specialists
inferred← citeshttps://doi.org/10.1038/s41564-018-0201-zopenalex-snapshot
Understanding how microbiomes influence the systems they inhabit
inferred← citeshttps://doi.org/10.1038/s41564-018-0276-6openalex-snapshot
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient
inferred← citeshttps://doi.org/10.1038/s41579-020-00458-8openalex-snapshot
Innovations to culturing the uncultured microbial majority
inferred← citeshttps://doi.org/10.1038/s41598-020-79143-yopenalex-snapshot
Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms
inferred← citeshttps://doi.org/10.1038/s41598-022-26810-xopenalex-snapshot
The rhizospheric bacterial diversity of Fritillaria taipaiensis under single planting pattern over five years
inferred← citeshttps://doi.org/10.1038/s41598-024-69673-0openalex-snapshot
Elucidating the interaction of rhizosphere microorganisms and environmental factors influencing the quality of Polygonatum kingianum Coll. et Hemsl.
inferred← citeshttps://doi.org/10.1038/s41598-025-85556-4openalex-snapshot
Trees shape the soil microbiome of a temperate agrosilvopastoral and syntropic agroforestry system
inferred← citeshttps://doi.org/10.1038/s43247-023-01020-zopenalex-snapshot
DNA sequencing, microbial indicators, and the discovery of buried kimberlites
inferred← citeshttps://doi.org/10.1038/s43705-021-00052-wopenalex-snapshot
Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species
inferred← citeshttps://doi.org/10.1038/s43705-022-00144-1openalex-snapshot
Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field
inferred← citeshttps://doi.org/10.1038/s43705-022-00209-1openalex-snapshot
Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils
inferred← citeshttps://doi.org/10.1038/srep45369openalex-snapshot
Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for
inferred← citeshttps://doi.org/10.1071/sr21112openalex-snapshot
Influences of grassland to cropland conversion on select soil properties, microbiome and agricultural emissions
inferred← citeshttps://doi.org/10.1073/pnas.2413032122openalex-snapshot
Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil
inferred← citeshttps://doi.org/10.1088/1755-1315/368/1/012030openalex-snapshot
Filtered forms of prokaryotes and bacteriophages in soil concretions
inferred← citeshttps://doi.org/10.1089/ast.2018.2012openalex-snapshot
Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region)
inferred← citeshttps://doi.org/10.1093/femsec/fiaa240openalex-snapshot
Many roads to bacterial generalism
inferred← citeshttps://doi.org/10.1093/femsec/fiab063openalex-snapshot
Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture
inferred← citeshttps://doi.org/10.1093/femsec/fiab148openalex-snapshot
Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns
inferred← citeshttps://doi.org/10.1093/femsec/fiad007openalex-snapshot
Restoration age and reintroduced bison may shape soil bacterial communities in restored tallgrass prairies
inferred← citeshttps://doi.org/10.1093/femsec/fiad161openalex-snapshot
Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves
inferred← citeshttps://doi.org/10.1093/femsmc/xtab020openalex-snapshot
Variation in genomic traits of microbial communities among ecosystems
inferred← citeshttps://doi.org/10.1093/femsre/fux039openalex-snapshot
Biophysical processes supporting the diversity of microbial life in soil
inferred← citeshttps://doi.org/10.1093/ismejo/wraf289openalex-snapshot
Constructing a “periodic table” of bacteria to map diversity in trait space
inferred← citeshttps://doi.org/10.1093/molbev/msab159openalex-snapshot
Enhanced Mutation Rate, Relaxed Selection, and the “Domino Effect” are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont
inferred← citeshttps://doi.org/10.1094/phytofr-03-25-0022-ropenalex-snapshot
Characterization of the Core Microbiome Associated with Table Beet Production in New York
inferred← citeshttps://doi.org/10.1099/ijsem.0.003789openalex-snapshot
Lists of names of prokaryotic Candidatus taxa
inferred← citeshttps://doi.org/10.1101/065128openalex-snapshot
Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework
inferred← citeshttps://doi.org/10.1101/150078openalex-snapshot
Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes
inferred← citeshttps://doi.org/10.1101/2021.01.09.426074openalex-snapshot
A non-adaptive demographic mechanism for genome expansion in Streptomyces
inferred← citeshttps://doi.org/10.1101/2021.04.29.442071openalex-snapshot
Stability of microbiota in vineyard soils across consecutive years
inferred← citeshttps://doi.org/10.1101/2021.08.22.456585openalex-snapshot
Soil inoculum identity and rate jointly steer microbiomes and plant communities in the field
inferred← citeshttps://doi.org/10.1101/2021.12.10.472086openalex-snapshot
Extreme drought triggers transition to an alternative soil microbial state
inferred← citeshttps://doi.org/10.1101/2022.02.03.479020openalex-snapshot
Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils
inferred← citeshttps://doi.org/10.1101/2024.04.13.589391openalex-snapshot
Challenging the impact of consortium diversity on bioaugmentation efficiency and native bacterial community structure in a freshly PAH-contaminated soil
inferred← citeshttps://doi.org/10.1101/2024.06.28.601247openalex-snapshot
Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil
inferred← citeshttps://doi.org/10.1101/2025.07.11.664459openalex-snapshot
A periodic table of bacteria?: Mapping bacterial diversity in trait space
inferred← citeshttps://doi.org/10.1101/2025.07.22.666192openalex-snapshot
A mismatch between slow protein synthesis and fast environmental fluctuations determines tradeoffs in bacterial proteome allocation strategies
inferred← citeshttps://doi.org/10.1101/570937openalex-snapshot
Changes in the Physicochemical Properties and Microbial Communities of Rhizospheric Soil after Cassava/Peanut Intercropping
inferred← citeshttps://doi.org/10.1111/1365-2745.13127openalex-snapshot
Contrasting patterns of plant and microbial diversity during long‐term ecosystem development
inferred← citeshttps://doi.org/10.1111/1462-2920.13785openalex-snapshot
Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27‐year chronosequence
inferred← citeshttps://doi.org/10.1111/1462-2920.14288openalex-snapshot
Novel bacterial lineages associated with boreal moss species
inferred← citeshttps://doi.org/10.1111/1462-2920.16074openalex-snapshot
Complex and flexible catabolism in Aromatoleum aromaticum pCyN1
inferred← citeshttps://doi.org/10.1111/1755-0998.12979openalex-snapshot
A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures
inferred← citeshttps://doi.org/10.1111/1758-2229.12880openalex-snapshot
Metagenome assembled‐genomes reveal similar functional profiles of CPR /Patescibacteria phyla in soils
inferred← citeshttps://doi.org/10.1111/1758-2229.13006openalex-snapshot
The ubiquitous soil verrucomicrobial clade ‘ Candidatus Udaeobacter’ shows preferences for acidic pH
inferred← citeshttps://doi.org/10.1111/ejss.12866openalex-snapshot
Dominant soil bacteria and their ecological attributes across the deserts in northern China
inferred← citeshttps://doi.org/10.1111/ejss.12977openalex-snapshot
Bacterial and archaeal taxa are reliable indicators of soil restoration across distributed calcareous grasslands
inferred← citeshttps://doi.org/10.1111/mec.14275openalex-snapshot
Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria
inferred← citeshttps://doi.org/10.1111/mec.16945openalex-snapshot
Soil depth and geographic distance modulate bacterial β‐diversity in deep soil profiles throughout the U.S. Corn Belt
inferred← citeshttps://doi.org/10.1111/sum.70251openalex-snapshot
Co‐Variation of Soil Chemistry, Bacterial Communities, and Functional Genes Under Different Tillage Systems in a Semiarid Agroecosystem
inferred← citeshttps://doi.org/10.1126/science.aap9516openalex-snapshot
A global atlas of the dominant bacteria found in soil
inferred← citeshttps://doi.org/10.1128/aem.01203-21openalex-snapshot
Adaptability of a Caproate-Producing Bacterium Contributes to Its Dominance in an Anaerobic Fermentation System
inferred← citeshttps://doi.org/10.1128/aem.01285-16openalex-snapshot
Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
inferred← citeshttps://doi.org/10.1128/aem.01635-24openalex-snapshot
Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities
inferred← citeshttps://doi.org/10.1128/aem.02673-20openalex-snapshot
The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa (United States)
inferred← citeshttps://doi.org/10.1128/genomea.00666-17openalex-snapshot
Draft Genome Sequence of Terrimicrobium sacchariphilum NM-5 T , a Facultative Anaerobic Soil Bacterium of the Class Spartobacteria
inferred← citeshttps://doi.org/10.1128/mbio.03099-20openalex-snapshot
Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil
inferred← citeshttps://doi.org/10.1128/mmbr.00124-22openalex-snapshot
A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments
inferred← citeshttps://doi.org/10.1128/msphere.00024-20openalex-snapshot
Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation
inferred← citeshttps://doi.org/10.1128/msphere.00186-20openalex-snapshot
Globally Abundant “ Candidatus Udaeobacter” Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging
inferred← citeshttps://doi.org/10.1128/msphere.00202-18openalex-snapshot
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria
inferred← citeshttps://doi.org/10.1128/msphere.00277-17openalex-snapshot
Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
inferred← citeshttps://doi.org/10.1128/msphere.00613-19openalex-snapshot
Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface
inferred← citeshttps://doi.org/10.1128/msystems.00153-19openalex-snapshot
Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers
inferred← citeshttps://doi.org/10.1128/msystems.00178-16openalex-snapshot
Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem
inferred← citeshttps://doi.org/10.1128/msystems.00574-22openalex-snapshot
Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis
inferred← citeshttps://doi.org/10.1128/spectrum.01234-22openalex-snapshot
Tripartite Symbiotic Digestion of Lignocellulose in the Digestive System of a Fungus-Growing Termite
inferred← citeshttps://doi.org/10.1139/cjm-2018-0612openalex-snapshot
Changes in microbial communities of a passive coal mine drainage bioremediation system
inferred← citeshttps://doi.org/10.11606/t.11.2021.tde-11052022-161255openalex-snapshot
Soil microbiological aspects upon the Fundão disaster
inferred← citeshttps://doi.org/10.1186/s12866-024-03238-zopenalex-snapshot
Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system
inferred← citeshttps://doi.org/10.1186/s12866-024-03432-zopenalex-snapshot
Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics
inferred← citeshttps://doi.org/10.1186/s12866-026-05335-7openalex-snapshot
Host species identity, compartment, and site jointly shape the bryophyte-associated bacterial communities in subtropical area
inferred← citeshttps://doi.org/10.1186/s12870-024-05415-8openalex-snapshot
Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms
inferred← citeshttps://doi.org/10.1186/s12896-020-00606-1openalex-snapshot
Cassava/peanut intercropping improves soil quality via rhizospheric microbes increased available nitrogen contents
inferred← citeshttps://doi.org/10.1186/s13568-018-0549-8openalex-snapshot
Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols
inferred← citeshttps://doi.org/10.1186/s40793-025-00696-4openalex-snapshot
Soil microbiome analysis of Uruguayan grasslands and croplands reveals losses of microbial diversity and necromass recycling traits
inferred← citeshttps://doi.org/10.1186/s40793-025-00752-zopenalex-snapshot
First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity
inferred← citeshttps://doi.org/10.1186/s40793-025-00790-7openalex-snapshot
Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil
inferred← citeshttps://doi.org/10.1360/tb-2021-0021openalex-snapshot
Habitat specificity and co-occurrence network of bacterial communities in the Xincuntun Cave, Guilin, Guangxi
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008866openalex-snapshot
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
inferred← citeshttps://doi.org/10.1371/journal.pone.0195112openalex-snapshot
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats
inferred← citeshttps://doi.org/10.1371/journal.pone.0237775openalex-snapshot
Diet type influences the gut microbiome and nutrient assimilation of Genetically Improved Farmed Tilapia (Oreochromis niloticus)
inferred← citeshttps://doi.org/10.1371/journal.pone.0242060openalex-snapshot
The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types
inferred← citeshttps://doi.org/10.1371/journal.pone.0251802openalex-snapshot
Correction: Diet type influences the gut microbiome and nutrient assimilation of Genetically Improved Farmed Tilapia (Oreochromis niloticus)
inferred← citeshttps://doi.org/10.15476/elte.2019.107openalex-snapshot
Az Ojos del Salado vulkán környéki magashegyi vizes élőhelyek extremofil baktériumközösségei
inferred← citeshttps://doi.org/10.1601/ex.33644openalex-snapshot
Exemplar Abstract for Udaeobacter copiosus Brewer et al. 2016.
inferred← citeshttps://doi.org/10.1601/nm.33643openalex-snapshot
Nomenclature Abstract for Udaeobacter Brewer et al. 2016.
inferred← citeshttps://doi.org/10.1601/nm.33644openalex-snapshot
Nomenclature Abstract for Udaeobacter copiosus Brewer et al. 2016.
inferred← citeshttps://doi.org/10.1601/tx.25460openalex-snapshot
Taxonomic Abstract for the families.
inferred← citeshttps://doi.org/10.1601/tx.33643openalex-snapshot
Taxonomic Abstract for the genera.
inferred← citeshttps://doi.org/10.1601/tx.33644openalex-snapshot
Taxonomic Abstract for the species.
inferred← citeshttps://doi.org/10.17037/pubs.04647551openalex-snapshot
Development of anaerobic culturing methods to study the evolution and of the human intestinal microbiota
inferred← citeshttps://doi.org/10.17116/molgen202543042177openalex-snapshot
Influence of perennial agrophytocenosis based on soil microbial parameters
inferred← citeshttps://doi.org/10.20417/nzjecol.44.22openalex-snapshot
Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1507219/v1openalex-snapshot
Loss of bacterial genetic diversity together with the increment of eutrophic and phytotoxic risk, the side effect of using raw poultry waste as soil amendment
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3345474/v1openalex-snapshot
Long-term Push-pull Cropping System Shifts Rhizosphere and Maize-root Microbiome Diversity Paving Way To Resilient Farming System
inferred← citeshttps://doi.org/10.21203/rs.3.rs-34776/v1openalex-snapshot
Functional selection associated with microbial genome size under polycyclic aromatic hydrocarbons (PAHs) pollution stress in soils
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4955337/v1openalex-snapshot
Soil Microbial Community Shifts in Rhizosphere and Original Soils during Two and Three Years of Ginseng Cultivation
inferred← citeshttps://doi.org/10.2139/ssrn.5912781openalex-snapshot
Nitrogen addition-induced variations in stoichiometric ratio of organic acids from litter decomposition in a temperate forest
inferred← citeshttps://doi.org/10.3103/s0891416825700508openalex-snapshot
Influence of Perennial Alfalfa-Based Agrophytocenoses on Soil Microbial Community Parameters
inferred← citeshttps://doi.org/10.31251/pos.v2i3.84openalex-snapshot
Taxonomic diversity of bacterial assemblage in technosol of the revegetating fly ash dump
inferred← citeshttps://doi.org/10.3389/feart.2021.598172openalex-snapshot
Methanogens and Their Syntrophic Partners Dominate Zones of Enhanced Magnetic Susceptibility at a Petroleum Contaminated Site
inferred← citeshttps://doi.org/10.3389/fmicb.2018.02732openalex-snapshot
Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects
inferred← citeshttps://doi.org/10.3389/fmicb.2019.01129openalex-snapshot
Global Biogeographic Distribution Patterns of Thermoacidophilic Verrucomicrobia Methanotrophs Suggest Allopatric Evolution
inferred← citeshttps://doi.org/10.3389/fmicb.2019.01955openalex-snapshot
Microbial Communities Associated With Passive Acidic Abandoned Coal Mine Remediation
inferred← citeshttps://doi.org/10.3389/fmicb.2021.636405openalex-snapshot
Impact of Rocky Desertification Control on Soil Bacterial Community in Karst Graben Basin, Southwestern China
inferred← citeshttps://doi.org/10.3389/fmicb.2021.682886openalex-snapshot
Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database
inferred← citeshttps://doi.org/10.3389/fmicb.2021.761869openalex-snapshot
A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy
inferred← citeshttps://doi.org/10.3389/fmicb.2022.933017openalex-snapshot
Endophytes and their potential in biotic stress management and crop production
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1220655openalex-snapshot
The core bacteriobiome of Côte d’Ivoire soils across three vegetation zones
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1285445openalex-snapshot
Stability of soil bacteria in undisturbed soil and continuous maize cultivation in Northern Thailand
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