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Progressive community, biogeochemical and evolutionary remodeling of the soil microbiome underpins long-term desert ecosystem restoration

https://doi.org/10.1101/2023.09.26.559499

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What this work says

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

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Dryland climate change: Recent progress and challenges

inferredcites →https://doi.org/10.1002/ldr.3690openalex-snapshot

Effects of vegetation restoration on soil nutrients, plant diversity, and its spatiotemporal heterogeneity in a desert–oasis ecotone

inferredcites →https://doi.org/10.1002/ldr.4045openalex-snapshot

Restoration of damaged ecosystems in desert steppe open‐pit coal mines: Effects on soil nematode communities and functions

inferredcites →https://doi.org/10.1007/978-981-13-7580-4openalex-snapshot

Remote Sensing of Land Use and Land Cover in Mountain Region

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AIC model selection and multimodel inference in behavioral ecology: some background, observations, and comparisons

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Proposed minimum reporting standards for chemical analysis

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Biofilm as an adaptation strategy to extreme conditions

inferredcites →https://doi.org/10.1007/s12665-018-7653-6openalex-snapshot

Quantitative analysis of how different checkerboard sand barrier materials influence soil properties: a study from the eastern edge of the Tengger Desert, China

inferredcites →https://doi.org/10.1016/b978-0-12-812060-6.00009-xopenalex-snapshot

Management Strategies for Organic Vegetable Fertility

inferredcites →https://doi.org/10.1016/bs.pmbts.2019.03.005openalex-snapshot

Clinical applications of the naturally occurring or synthetic glycosylated low molecular weight drugs

inferredcites →https://doi.org/10.1016/j.apsoil.2022.104394openalex-snapshot

Shift in soil microbial communities along ~160 years of natural vegetation restoration on the Loess Plateau of China

inferredcites →https://doi.org/10.1016/j.biosystemseng.2013.06.008openalex-snapshot

Getting simultaneous red and near-infrared band data from a single digital camera for plant monitoring applications: Theoretical and practical study

inferredcites →https://doi.org/10.1016/j.cell.2018.08.060openalex-snapshot

Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

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Methanogenesis

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Developing good practice guidance for estimating land degradation in the context of the United Nations Sustainable Development Goals

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Mucoromycota: going to the roots of plant-interacting fungi

inferredcites →https://doi.org/10.1016/j.geoderma.2012.10.018openalex-snapshot

Carbon accumulation in Icelandic desert Andosols during early stages of restoration

inferredcites →https://doi.org/10.1016/j.geoderma.2021.115369openalex-snapshot

Biocrust and the soil surface: Influence of climate, disturbance, and biocrust recovery on soil surface roughness

inferredcites →https://doi.org/10.1016/j.jenvman.2019.04.108openalex-snapshot

Vegetation restoration drives the dynamics and distribution of nitrogen and phosphorous pools in a temperate desert soil-plant system

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TaxonKit: A practical and efficient NCBI taxonomy toolkit

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Measuring the size of non-spherical particles and the implications for grain size analysis in volcanology

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Pollution impact on microbial communities composition in natural and anthropogenically modified soils of Southern Russia

inferredcites →https://doi.org/10.1016/j.pedobi.2020.150668openalex-snapshot

Climate and soil properties regulate soil fungal communities on the Loess Plateau

inferredcites →https://doi.org/10.1016/j.rala.2022.01.003openalex-snapshot

Four paths toward realizing the full potential of using native plants during ecosystem restoration in the Intermountain West

inferredcites →https://doi.org/10.1016/j.soilbio.2014.10.007openalex-snapshot

Untargeted soil metabolomics methods for analysis of extractable organic matter

inferredcites →https://doi.org/10.1016/j.soilbio.2019.05.004openalex-snapshot

Changes in microbial functional genes within the soil metagenome during forest ecosystem restoration

inferredcites →https://doi.org/10.1016/j.soilbio.2019.107584openalex-snapshot

pH and exchangeable aluminum are major regulators of microbial energy flow and carbon use efficiency in soil microbial communities

inferredcites →https://doi.org/10.1016/j.soilbio.2020.107758openalex-snapshot

Use of untargeted metabolomics for assessing soil quality and microbial function

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Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples

inferredcites →https://doi.org/10.1017/cbo9781139627061openalex-snapshot

Multivariate Analysis of Ecological Data using CANOCO 5

inferredcites →https://doi.org/10.1021/acs.analchem.1c02687openalex-snapshot

SLAW: A Scalable and Self-Optimizing Processing Workflow for Untargeted LC-MS

inferredcites →https://doi.org/10.1021/acs.analchem.9b04804openalex-snapshot

AutoTuner: High Fidelity and Robust Parameter Selection for Metabolomics Data Processing

inferredcites →https://doi.org/10.1029/2007gl031725openalex-snapshot

Long‐term effects of restoration on soil hydraulic properties in revegetation‐stabilized desert ecosystems

inferredcites →https://doi.org/10.1038/ismej.2012.22openalex-snapshot

Stochastic and deterministic assembly processes in subsurface microbial communities

inferredcites →https://doi.org/10.1038/ismej.2013.93openalex-snapshot

Quantifying community assembly processes and identifying features that impose them

inferredcites →https://doi.org/10.1038/ismej.2017.126openalex-snapshot

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

inferredcites →https://doi.org/10.1038/ismej.2017.91openalex-snapshot

Cohesion: a method for quantifying the connectivity of microbial communities

inferredcites →https://doi.org/10.1038/nature12375openalex-snapshot

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

inferredcites →https://doi.org/10.1038/nbt.2377openalex-snapshot

A cross-platform toolkit for mass spectrometry and proteomics

inferredcites →https://doi.org/10.1038/nbt.3597openalex-snapshot

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

inferredcites →https://doi.org/10.1038/nbt.3893openalex-snapshot

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

inferredcites →https://doi.org/10.1038/nrm1524openalex-snapshot

Making sense of it all: bacterial chemotaxis

inferredcites →https://doi.org/10.1038/nrmicro1852openalex-snapshot

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

inferredcites →https://doi.org/10.1038/s41396-022-01238-3openalex-snapshot

Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome

inferredcites →https://doi.org/10.1038/s41467-017-02356-9openalex-snapshot

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

inferredcites →https://doi.org/10.1038/s41467-020-20241-wopenalex-snapshot

Perineuronal nets stabilize the grid cell network

inferredcites →https://doi.org/10.1038/s41467-022-28581-5openalex-snapshot

Genome binning of viral entities from bulk metagenomics data

inferredcites →https://doi.org/10.1038/s41467-022-29843-yopenalex-snapshot

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

inferredcites →https://doi.org/10.1038/s41522-021-00263-yopenalex-snapshot

Microbial co-occurrence network topological properties link with reactor parameters and reveal importance of low-abundance genera

inferredcites →https://doi.org/10.1038/s41564-018-0171-1openalex-snapshot

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

inferredcites →https://doi.org/10.1038/s41564-022-01203-yopenalex-snapshot

Wildfire-dependent changes in soil microbiome diversity and function

inferredcites →https://doi.org/10.1038/s41586-018-0386-6openalex-snapshot

Structure and function of the global topsoil microbiome

inferredcites →https://doi.org/10.1038/s41587-020-00797-0openalex-snapshot

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

inferredcites →https://doi.org/10.1038/s41592-019-0344-8openalex-snapshot

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

inferredcites →https://doi.org/10.1038/s41592-021-01101-xopenalex-snapshot

Sensitive protein alignments at tree-of-life scale using DIAMOND

inferredcites →https://doi.org/10.1038/s41596-020-00451-8openalex-snapshot

Decoding personal biotic and abiotic airborne exposome

inferredcites →https://doi.org/10.1038/s41893-019-0220-7openalex-snapshot

China and India lead in greening of the world through land-use management

inferredcites →https://doi.org/10.1038/s43017-022-00366-wopenalex-snapshot

Soil structure and microbiome functions in agroecosystems

inferredcites →https://doi.org/10.1039/d1np00028dopenalex-snapshot

Recent advances in the synthesis of ent -kaurane diterpenoids

inferredcites →https://doi.org/10.1073/pnas.0406811102openalex-snapshot

Uncovering transcriptional regulation of metabolism by using metabolic network topology

inferredcites →https://doi.org/10.1073/pnas.0706375104openalex-snapshot

The modularity of pollination networks

inferredcites →https://doi.org/10.1073/pnas.1402028111openalex-snapshot

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO 2 fixation

inferredcites →https://doi.org/10.1073/pnas.1405637111openalex-snapshot

The transition between the niche and neutral regimes in ecology

inferredcites →https://doi.org/10.1073/pnas.1509788112openalex-snapshot

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

inferredcites →https://doi.org/10.1073/pnas.1609534113openalex-snapshot

Archaea catalyze iron-dependent anaerobic oxidation of methane

inferredcites →https://doi.org/10.1073/pnas.1815631116openalex-snapshot

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

inferredcites →https://doi.org/10.1074/jbc.m112.413195openalex-snapshot

Role of 4-Hydroxybutyrate-CoA Synthetase in the CO2 Fixation Cycle in Thermoacidophilic Archaea

inferredcites →https://doi.org/10.1088/0256-307x/27/7/078902openalex-snapshot

Natural Connectivity of Complex Networks

inferredcites →https://doi.org/10.1093/bioinformatics/btac726openalex-snapshot

RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes

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APE: Analyses of Phylogenetics and Evolution in R language

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

inferredcites →https://doi.org/10.1093/bioinformatics/bty741openalex-snapshot

NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

inferredcites →https://doi.org/10.1093/bioinformatics/btz848openalex-snapshot

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

inferredcites →https://doi.org/10.1093/femsre/fuu011openalex-snapshot

Microbial ecology of hot desert edaphic systems

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/msab166openalex-snapshot

ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data

inferredcites →https://doi.org/10.1093/nar/gkaa946openalex-snapshot

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

inferredcites →https://doi.org/10.1093/nar/gkab1045openalex-snapshot

The carbohydrate-active enzyme database: functions and literature

inferredcites →https://doi.org/10.1093/nar/gkab301openalex-snapshot

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

inferredcites →https://doi.org/10.1093/nar/gki008openalex-snapshot

VFDB: a reference database for bacterial virulence factors

inferredcites →https://doi.org/10.1093/nar/gkp829openalex-snapshot

Sequence-non-specific effects of RNA interference triggers and microRNA regulators

inferredcites →https://doi.org/10.1093/nar/gks479openalex-snapshot

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

inferredcites →https://doi.org/10.1098/rspb.2013.2728openalex-snapshot

Statistical methods for temporal and space–time analysis of community composition data

inferredcites →https://doi.org/10.1099/ijs.0.053082-0openalex-snapshot

Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil

inferredcites →https://doi.org/10.1099/ijs.0.058396-0openalex-snapshot

Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter

inferredcites →https://doi.org/10.1099/ijsem.0.001272openalex-snapshot

Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert

inferredcites →https://doi.org/10.1099/ijsem.0.001916openalex-snapshot

Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil

inferredcites →https://doi.org/10.1099/ijsem.0.005009openalex-snapshot

Massilia rhizosphaerae sp. nov., a rice-associated rhizobacterium with antibacterial activity against Ralstonia solanacearum

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/10.1103/physreve.70.066111openalex-snapshot

Finding community structure in very large networks

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A Generalisation Of The Fuzzy C-means Clustering Algorithm

inferredcites →https://doi.org/10.1111/1755-0998.13306openalex-snapshot

SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways

inferredcites →https://doi.org/10.1111/1755-0998.13589openalex-snapshot

MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes

inferredcites →https://doi.org/10.1111/geb.13173openalex-snapshot

Contrasting environmental preferences of photosynthetic and non‐photosynthetic soil cyanobacteria across the globe

inferredcites →https://doi.org/10.1111/j.1462-2920.2005.00956.xopenalex-snapshot

Quantifying the roles of immigration and chance in shaping prokaryote community structure

inferredcites →https://doi.org/10.1111/j.1600-0587.2010.06548.xopenalex-snapshot

Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities

inferredcites →https://doi.org/10.1111/mec.14914openalex-snapshot

Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions

inferredcites →https://doi.org/10.1111/nph.18095openalex-snapshot

Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

inferredcites →https://doi.org/10.1111/rec.13115openalex-snapshot

Biological soil crust salvage for dryland restoration: an opportunity for natural resource restoration

inferredcites →https://doi.org/10.1126/science.aaa1185openalex-snapshot

Disentangling global soil fungal diversity

inferredcites →https://doi.org/10.1126/science.abe0725openalex-snapshot

Soil microbiota as game-changers in restoration of degraded lands

inferredcites →https://doi.org/10.1128/aac.00419-13openalex-snapshot

The Comprehensive Antibiotic Resistance Database

inferredcites →https://doi.org/10.1128/aem.02473-10openalex-snapshot

Ecological Aspects of the Distribution of Different Autotrophic CO 2 Fixation Pathways

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In Situ Characterization of Nitrospira -Like Nitrite-Oxidizing Bacteria Active in Wastewater Treatment Plants

inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot

Kraken: ultrafast metagenomic sequence classification using exact alignments

inferredcites →https://doi.org/10.1186/s12859-015-0562-8openalex-snapshot

IPO: a tool for automated optimization of XCMS parameters

inferredcites →https://doi.org/10.1186/s12859-019-3031-yopenalex-snapshot

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

inferredcites →https://doi.org/10.1186/s40168-019-0684-8openalex-snapshot

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

inferredcites →https://doi.org/10.1186/s40168-022-01292-1openalex-snapshot

PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes

inferredcites →https://doi.org/10.1186/s40793-023-00463-3openalex-snapshot

Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems

inferredcites →https://doi.org/10.1196/annals.1419.000openalex-snapshot

Methane as Fuel for Anaerobic Microorganisms

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Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

inferredcites →https://doi.org/10.1371/journal.pgen.1002441openalex-snapshot

Diverse CRISPRs Evolving in Human Microbiomes

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phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

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metaSNV: A tool for metagenomic strain level analysis

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Monitoring vegetation coverage in Tongren from 2000 to 2016 based on Landsat7 ETM+ and Landsat8

inferredcites →https://doi.org/10.18103/mra.v8i7.2169openalex-snapshot

"Desert Chemotypes": The Potential of Desert Plants-Derived Metabolome to Become a Sustainable Resource for Drug Leads

inferredcites →https://doi.org/10.2136/sssaj2001.653849xopenalex-snapshot

Simplified Method for Soil Particle‐Size Determination to Accompany Soil‐Quality Analyses

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Elemental Sulfur Oxidation in Australian Cropping Soils

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One Juliet and four Romeos: VeA and its methyltransferases

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Rarefaction, Alpha Diversity, and Statistics

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Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments

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Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development

inferredcites →https://doi.org/10.3390/agriculture11070626openalex-snapshot

Revisiting Sulphur—The Once Neglected Nutrient: It’s Roles in Plant Growth, Metabolism, Stress Tolerance and Crop Production

inferredcites →https://doi.org/10.3390/antibiotics8010018openalex-snapshot

CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool

inferredcites →https://doi.org/10.3390/molecules22020281openalex-snapshot

Hydroxycinnamic Acids and Their Derivatives: Cosmeceutical Significance, Challenges and Future Perspectives, a Review

inferredcites →https://doi.org/10.5194/bg-8-2907-2011openalex-snapshot

Phosphorus transformations as a function of pedogenesis: A synthesis of soil phosphorus data using Hedley fractionation method

inferredcites →https://doi.org/10.5772/61629openalex-snapshot

Land Degradation and Desertification - a Global Crisis

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Compact graphical representation of phylogenetic data and metadata with GraPhlAn

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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

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Texture Influence on Soil Phosphorus Content and Distribution in Semiarid Pampean Grasslands

What points at this work

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

inferred← citeshttps://doi.org/10.1093/bib/bbag119openalex-snapshot

Kun-peng enables scalable and accurate pan-domain metagenomic classification

inferred← citeshttps://doi.org/10.1093/jambio/lxaf262openalex-snapshot

Impact of ecological restoration on the soil microbial communities during the restoration of damaged mountain slope in China’s Heilong River Basin

inferred← citeshttps://doi.org/10.1101/2024.12.19.629356openalex-snapshot

Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all

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