The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity.

[1]  Zhili He,et al.  Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes , 2023, Microbiome.

[2]  Meng Li,et al.  Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems. , 2023, Journal of environmental management.

[3]  Zhili He,et al.  PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes , 2022, Microbiome.

[4]  X. Yi,et al.  Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes , 2022, The ISME Journal.

[5]  M. Gillings,et al.  Assessment of global health risk of antibiotic resistance genes , 2022, Nature Communications.

[6]  Charmaine Ng,et al.  Population-based variations of a core resistome revealed by urban sewage metagenome surveillance. , 2022, Environment international.

[7]  D. Khasa,et al.  Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes. , 2022, The Science of the total environment.

[8]  Seung Chul Shin,et al.  Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics. , 2021, Environmental pollution.

[9]  Chen Wang,et al.  Evidence for Long-Term Anthropogenic Pollution: The Hadal Trench as a Depository and Indicator for Dissemination of Antibiotic Resistance Genes. , 2021, Environmental science & technology.

[10]  Zhili He,et al.  Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments , 2021, Microbiome.

[11]  J. W. Turner,et al.  Bioplastic accumulates antibiotic and metal resistance genes in coastal marine sediments. , 2021, Environmental pollution.

[12]  Siyuan Ma,et al.  Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities - A study in Hainan Island, China. , 2021, Environmental pollution.

[13]  W. Hanage,et al.  Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes , 2021, Proceedings of the National Academy of Sciences.

[14]  Michael L. Whittaker,et al.  Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems , 2021, Nature Microbiology.

[15]  S. Wang,et al.  Antibiotics in marine aquaculture farms surrounding Laizhou Bay, Bohai Sea: Distribution characteristics considering various culture modes and organism species. , 2020, The Science of the total environment.

[16]  M. Imchen,et al.  Metagenomic insights into the antibiotic resistome of mangrove sediments and their association to socioeconomic status. , 2020, Environmental pollution.

[17]  Xiaowei Zhang,et al.  Human activities' fingerprint on multitrophic biodiversity and ecosystem functions across a major river catchment in China , 2020, Global change biology.

[18]  Zhong Hu,et al.  Diversity and distribution of antibiotics and antibiotic resistance genes in seven national mangrove nature reserves, South China , 2020 .

[19]  M. Imchen,et al.  Shotgun metagenomics reveals heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediments. , 2020, FEMS microbiology ecology.

[20]  Q. Wen,et al.  Impacts of Cu and Zn on the performance, microbial community dynamics and resistance genes variations during mesophilic and thermophilic anaerobic digestion of swine manure. , 2020, Bioresource technology.

[21]  B. Baker,et al.  Diversity, ecology and evolution of Archaea , 2020, Nature Microbiology.

[22]  R. Zuo,et al.  Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system. , 2020, Environment international.

[23]  Geoffrey L. Winsor,et al.  CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database , 2019, Nucleic Acids Res..

[24]  J. Sparks,et al.  Non‐native mangroves support carbon storage, sediment carbon burial, and accretion of coastal ecosystems , 2019, Global change biology.

[25]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[26]  N. Fierer,et al.  High proportions of bacteria and archaea across most biomes remain uncultured , 2019, The ISME Journal.

[27]  J. Peñuelas,et al.  Loss of soil microbial diversity exacerbates spread of antibiotic resistance , 2019, Soil Ecology Letters.

[28]  Zhang Ke-li,et al.  Estimating long-term erosion and sedimentation rate on farmland using magnetic susceptibility in northeast China , 2019, Soil and Tillage Research.

[29]  Z. Zeng,et al.  Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments. , 2019, Environment international.

[30]  M. Bhattacharyya,et al.  Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India. , 2019, The Science of the total environment.

[31]  H. Bürgmann,et al.  Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes , 2018, The ISME Journal.

[32]  J. Bengtsson-Palme,et al.  Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements , 2018, Nature Communications.

[33]  Tong Zhang,et al.  Tracking antibiotic resistance gene pollution from different sources using machine-learning classification , 2018, Microbiome.

[34]  Mingqing Pan,et al.  Occurrence of antibiotics and antibiotic resistance genes in soils from wastewater irrigation areas in the Pearl River Delta region, southern China. , 2018, The Science of the total environment.

[35]  E. Garner,et al.  DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data , 2018, Microbiome.

[36]  Tong Zhang,et al.  Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey , 2017, Microbiome.

[37]  Charmaine Ng,et al.  Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters , 2017, Front. Microbiol..

[38]  Qingxiang Yang,et al.  Molecular characterization of antibiotic resistance in cultivable multidrug-resistant bacteria from livestock manure. , 2017, Environmental pollution.

[39]  R. E. Collins,et al.  Effect of the environment on horizontal gene transfer between bacteria and archaea , 2017, PeerJ.

[40]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[41]  Tong Zhang,et al.  Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection , 2016, The ISME Journal.

[42]  M. Hess,et al.  Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities. , 2016, Environmental pollution.

[43]  Hing-Fung Ting,et al.  MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. , 2016, Methods.

[44]  M. V. D. van der Heijden,et al.  An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability. , 2016, Trends in ecology & evolution.

[45]  Brian C. Thomas,et al.  A new view of the tree of life , 2016, Nature Microbiology.

[46]  Luke S P Moore,et al.  Antimicrobials: access and sustainable eff ectiveness 2 Understanding the mechanisms and drivers of antimicrobial resistance , 2015 .

[47]  Bing Li,et al.  Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces. , 2016, Environmental science & technology.

[48]  Erik Kristiansson,et al.  Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential , 2015, BMC Genomics.

[49]  Ming Liu,et al.  Effects of long-term manure applications on the occurrence of antibiotics and antibiotic resistance genes (ARGs) in paddy soils: Evidence from four field experiments in south of China , 2015 .

[50]  Teresa M. Coque,et al.  What is a resistance gene? Ranking risk in resistomes , 2014, Nature Reviews Microbiology.

[51]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[52]  Y. Tor,et al.  Antibiotics and Bacterial Resistance in the 21st Century , 2014, Perspectives in medicinal chemistry.

[53]  Molly K. Gibson,et al.  Bacterial phylogeny structures soil resistomes across habitats , 2014, Nature.

[54]  R. De la Iglesia,et al.  Heavy metal concentration in mangrove surface sediments from the north-west coast of South America. , 2014, Marine pollution bulletin.

[55]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[56]  M. V. D. van der Heijden,et al.  Soil biodiversity and soil community composition determine ecosystem multifunctionality , 2014, Proceedings of the National Academy of Sciences.

[57]  D. Alongi Carbon cycling and storage in mangrove forests. , 2014, Annual review of marine science.

[58]  Erik Kristiansson,et al.  BacMet: antibacterial biocide and metal resistance genes database , 2013, Nucleic Acids Res..

[59]  M. Popowska,et al.  Broad-host-range IncP-1 plasmids and their resistance potential , 2013, Front. Microbiol..

[60]  H. Thatoi,et al.  Biodiversity and biotechnological potential of microorganisms from mangrove ecosystems: a review , 2013, Annals of Microbiology.

[61]  Timothy A. Johnson,et al.  Diverse and abundant antibiotic resistance genes in Chinese swine farms , 2013, Proceedings of the National Academy of Sciences.

[62]  P. Alvarez,et al.  Tetracycline resistance gene maintenance under varying bacterial growth rate, substrate and oxygen availability, and tetracycline concentration. , 2013, Environmental science & technology.

[63]  Mazdak Arabi,et al.  Correlation between upstream human activities and riverine antibiotic resistance genes. , 2012, Environmental science & technology.

[64]  A. Teske,et al.  Microbial diversity and stratification of South Pacific abyssal marine sediments. , 2011, Environmental microbiology.

[65]  Xing-li Sun,et al.  Antibiotic resistance of bacteria isolated from shrimp hatcheries and cultural ponds on Donghai Island, China. , 2011, Marine pollution bulletin.

[66]  S. Schuster,et al.  Integrative analysis of environmental sequences using MEGAN4. , 2011, Genome research.

[67]  B. Cui,et al.  Assessment of heavy metal pollution in wetland soils from the young and old reclaimed regions in the Pearl River Estuary, South China. , 2011, Environmental pollution.

[68]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[69]  A. Sapkota,et al.  Aquaculture practices and potential human health risks: current knowledge and future priorities. , 2008, Environment international.

[70]  S. Allison,et al.  Resistance, resilience, and redundancy in microbial communities , 2008, Proceedings of the National Academy of Sciences.

[71]  Y. Topalova,et al.  Survival of genetically marked Escherichia coli O157:H7 in soil as affected by soil microbial community shifts , 2007, The ISME Journal.

[72]  C. Stamm,et al.  Depth distribution of sulfonamide antibiotics in pore water of an undisturbed loamy grassland soil. , 2007, Journal of environmental quality.

[73]  Didier Mazel,et al.  Integrons: agents of bacterial evolution , 2006, Nature Reviews Microbiology.

[74]  Ramunas Stepanauskas,et al.  Co-selection of antibiotic and metal resistance. , 2006, Trends in microbiology.

[75]  Hector M Guzman,et al.  An assessment of metal contamination in mangrove sediments and leaves from Punta Mala Bay, Pacific Panama. , 2005, Marine pollution bulletin.

[76]  T. Glenn,et al.  Elevated microbial tolerance to metals and antibiotics in metal-contaminated industrial environments. , 2005, Environmental science & technology.

[77]  J. Tiedje,et al.  DNA recovery from soils of diverse composition , 1996, Applied and environmental microbiology.