Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Microbiome
2024 Feb 14;121:27. doi: 10.1186/s40168-024-01759-3.
Show Gene links
Show Anatomy links
Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones.
Sun H
,
Wang T
,
Liu S
,
Tang X
,
Sun J
,
Liu X
,
Zhao Y
,
Shen P
,
Zhang Y
.
Abstract
BACKGROUND: Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors.
RESULTS: Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones.
CONCLUSIONS: Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract.
Adams,
Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances.
2013, Pubmed
Adams,
Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances.
2013,
Pubmed
Ahmed,
Adsorptive removal of antibiotics from water and wastewater: Progress and challenges.
2015,
Pubmed
Begmatov,
Microbial Communities Involved in Methane, Sulfur, and Nitrogen Cycling in the Sediments of the Barents Sea.
2021,
Pubmed
Beiralas,
Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria.
2023,
Pubmed
Bolyen,
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
2019,
Pubmed
Brodersen,
Seagrass rhizosphere microenvironment alters plant-associated microbial community composition.
2018,
Pubmed
Buchfink,
Fast and sensitive protein alignment using DIAMOND.
2015,
Pubmed
Buck-Wiese,
Fucoid brown algae inject fucoidan carbon into the ocean.
2023,
Pubmed
Callahan,
DADA2: High-resolution sample inference from Illumina amplicon data.
2016,
Pubmed
Canion,
Isolation and physiological characterization of psychrophilic denitrifying bacteria from permanently cold Arctic fjord sediments (Svalbard, Norway).
2013,
Pubmed
Chaumeil,
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
2019,
Pubmed
Chen,
fastp: an ultra-fast all-in-one FASTQ preprocessor.
2018,
Pubmed
Chia,
Lipid composition of Chlorella vulgaris (Trebouxiophyceae) as a function of different cadmium and phosphate concentrations.
2013,
Pubmed
Crump,
Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes.
2018,
Pubmed
Dong,
Cultivable alginate lyase-excreting bacteria associated with the Arctic brown alga Laminaria.
2012,
Pubmed
Donnelly,
Bacterial interactions in the rhizosphere of seagrass communities in shallow coastal lagoons.
1998,
Pubmed
Edwards,
Structure, variation, and assembly of the root-associated microbiomes of rice.
2015,
Pubmed
Ettinger,
Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina.
2020,
Pubmed
Ettinger,
Characterization of the Mycobiome of the Seagrass, Zostera marina, Reveals Putative Associations With Marine Chytrids.
2019,
Pubmed
Ettinger,
Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge.
2017,
Pubmed
Fahimipour,
Global-Scale Structure of the Eelgrass Microbiome.
2017,
Pubmed
Firpo,
Diverse Functions of Polyamines in Virus Infection.
2020,
Pubmed
Fu,
CD-HIT: accelerated for clustering the next-generation sequencing data.
2012,
Pubmed
Gao,
Occurrence of sulfonamide and tetracycline-resistant bacteria and resistance genes in aquaculture environment.
2012,
Pubmed
Grossart,
Fungi in aquatic ecosystems.
2019,
Pubmed
He,
Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture.
2022,
Pubmed
Hurtado-McCormick,
Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome.
2019,
Pubmed
Inagaki,
Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa Trough hydrothermal sediments.
2004,
Pubmed
Jia,
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
2017,
Pubmed
Kanehisa,
KEGG: kyoto encyclopedia of genes and genomes.
2000,
Pubmed
Kang,
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
2015,
Pubmed
Kang,
The impact of mariculture on nutrient dynamics and identification of the nitrate sources in coastal waters.
2016,
Pubmed
,
Echinobase
Komova,
Nitrogen Fixation Activity and Genome Analysis of a Moderately Haloalkaliphilic Anoxygenic Phototrophic Bacterium Rhodovulum tesquicola.
2022,
Pubmed
Kumari,
Nitrate and phosphate regimes induced lipidomic and biochemical changes in the intertidal macroalga Ulva lactuca (Ulvophyceae, Chlorophyta).
2014,
Pubmed
Lawson,
Metabolic network analysis reveals microbial community interactions in anammox granules.
2017,
Pubmed
Lehnen,
High rates of microbial dinitrogen fixation and sulfate reduction associated with the Mediterranean seagrass Posidonia oceanica.
2016,
Pubmed
Li,
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
2015,
Pubmed
Li,
Fast and accurate short read alignment with Burrows-Wheeler transform.
2009,
Pubmed
Lin,
Integrative metabolic and microbial profiling on patients with Spleen-yang-deficiency syndrome.
2018,
Pubmed
Lin,
Alkaline Phosphatase Gene Sequence And Transcriptional Regulation By Phosphate Limitation In Amphidinium Carterae (Dinophyceae)(1).
2011,
Pubmed
Lindsey,
Wolbachia and Virus Alter the Host Transcriptome at the Interface of Nucleotide Metabolism Pathways.
2021,
Pubmed
Liu,
Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients.
2015,
Pubmed
Liu,
Physicochemical characterization and cosmetic application of kelp blanching water polysaccharides.
2023,
Pubmed
Ma,
Fabrication of magnetic molecularly imprinted polymers based on aptamers and β-cyclodextrin for synergistic recognition and separation of tetracycline.
2022,
Pubmed
Magoč,
FLASH: fast length adjustment of short reads to improve genome assemblies.
2011,
Pubmed
Martin,
Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots.
2017,
Pubmed
Martin,
Oxygen loss from seagrass roots coincides with colonisation of sulphide-oxidising cable bacteria and reduces sulphide stress.
2019,
Pubmed
Martinez,
Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments.
2014,
Pubmed
Mohapatra,
Seagrasses and local environment control the bacterial community structure and carbon substrate utilization in brackish sediments.
2022,
Pubmed
Naylor,
A 20-year retrospective review of global aquaculture.
2021,
Pubmed
Nielsen,
Sulphate reduction and nitrogen fixation rates associated with roots, rhizomes and sediments from Zostera noltii and Spartina maritima meadows.
2001,
Pubmed
O'Donohue,
Nitrogen fixation in sediments and the rhizosphere of the seagrassZostera capricorni.
1991,
Pubmed
Parks,
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
2015,
Pubmed
Peay,
Dimensions of biodiversity in the Earth mycobiome.
2016,
Pubmed
Pelikan,
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment.
2021,
Pubmed
Peng,
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
2012,
Pubmed
Pitt,
Aquiluna borgnonia gen. nov., sp. nov., a member of a Microbacteriaceae lineage of freshwater bacteria with small genome sizes.
2021,
Pubmed
Segata,
Metagenomic biomarker discovery and explanation.
2011,
Pubmed
Selvarajan,
Distribution, Interaction and Functional Profiles of Epiphytic Bacterial Communities from the Rocky Intertidal Seaweeds, South Africa.
2019,
Pubmed
Serra,
Influence of phosphorus on copper sensitivity of fluvial periphyton: the role of chemical, physiological and community-related factors.
2010,
Pubmed
Shang,
Studies on the Composition and Diversity of Seagrass Ruppia sinensis Rhizosphere Mmicroorganisms in the Yellow River Delta.
2023,
Pubmed
Stoeck,
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water.
2010,
Pubmed
Sun,
Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary.
2021,
Pubmed
Sun,
Kelp Culture Enhances Coastal Biogeochemical Cycles by Maintaining Bacterioplankton Richness and Regulating Its Interactions.
2023,
Pubmed
Sánchez-Cañizares,
Understanding the holobiont: the interdependence of plants and their microbiome.
2017,
Pubmed
Tarquinio,
The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning.
2019,
Pubmed
Tarquinio,
Microorganisms facilitate uptake of dissolved organic nitrogen by seagrass leaves.
2018,
Pubmed
Trevizan Segovia,
Microeukaryotic Communities Associated With the Seagrass Zostera marina Are Spatially Structured.
2021,
Pubmed
Ugarelli,
The Seagrass Holobiont and Its Microbiome.
2017,
Pubmed
Wainwright,
Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration.
2019,
Pubmed
Walls,
Impact of kelp cultivation on the Ecological Status of benthic habitats and Zostera marina seagrass biomass.
2017,
Pubmed
Wang,
Nutrient enrichment increases size of Zostera marina shoots and enriches for sulfur and nitrogen cycling bacteria in root-associated microbiomes.
2020,
Pubmed
Wang,
Antibiotics in mariculture systems: A review of occurrence, environmental behavior, and ecological effects.
2022,
Pubmed
Wang,
Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems.
2018,
Pubmed
Wang,
Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area.
2020,
Pubmed
Wang,
Cloning and characterization of nitrate reductase gene in kelp Saccharina japonica (Laminariales, Phaeophyta).
2023,
Pubmed
Weigel,
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes.
2022,
Pubmed
Weitzman,
Virus DNA Replication and the Host DNA Damage Response.
2018,
Pubmed
Zai,
Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.
2021,
Pubmed
Zecher,
Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere.
2020,
Pubmed
Zhang,
Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome.
2017,
Pubmed
Zhang,
Rhizosphere Microbial Community Structure Is Selected by Habitat but Not Plant Species in Two Tropical Seagrass Beds.
2020,
Pubmed
Zhao,
Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture.
2017,
Pubmed
Zhao,
Effects of river damming and delta erosion on organic carbon burial in the Changjiang Estuary and adjacent East China Sea inner shelf.
2021,
Pubmed
