Differential microbial assembly processes and co‐occurrence networks in the soil‐root continuum along an environmental gradient

iMeta, Journal Year: 2022, Volume and Issue: 1(2)

Published: April 5, 2022

Abstract Microorganisms of the soil‐root continuum play key roles in ecosystem function. The Loess Plateau is well known for its severe soil erosion and thick loess worldwide, where mean annual precipitation (MAP) nutrients decrease from southeast to northwest. However, relative influence environmental factors on microbial community four microhabitats (bulk soil, rhizosphere, rhizoplane, endosphere) along gradient remains unclear. In this study, we investigated 82 field sites warm‐temperate desert grasslands across Plateau, China, assess bacterial diversity, composition, assembly, co‐occurrence networks an using 16S recombinant DNA amplicon sequencing. We discovered that explained largest source variations diversity composition region. Environmental (e.g., MAP, organic carbon, pH) impacted rhizoplane communities, but their effects decreased with increased proximity roots MAP enlarged dissimilarity communities rhizosphere bulk soil. Additionally, stochastic assembly processes drove endosphere whereas were governed primarily by variable selection deterministic processes, which showed importance grasslands. Moreover, properties indicate more stable grasslands, likely conferring resistance higher stress environments. Collectively, our results had different sensitivities mechanisms gradient. These patterns are shaped simultaneously intertwined dimensions change Plateau.

Language: Английский

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Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: April 5, 2023

Abstract Background Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism microbially driven cycling along sediment depth mangrove wetlands remain elusive. Here we investigated vertical profile methane (CH 4 ), nitrogen (N) sulphur (S) genes/pathways their potential mechanisms using metagenome sequencing approaches. Results Our results showed that metabolic pathways involved in CH , N S were mainly shaped by pH acid volatile sulphide (AVS) a depth, AVS was critical electron donor impacting oxidation denitrification. Gene families denitrification significantly ( P < 0.05) decreased could be coupled S-driven denitrifiers, such Burkholderiaceae Sulfurifustis surface (0–15 cm). Interestingly, all denitrifier metagenome-assembled genomes (MAGs) appeared to incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous reductase (Nos), suggesting sulphide-utilizing groups might an important contributor 2 O production sediment. methanogenesis reduction increased depth. Based on both network MAG analyses, sulphate-reducing bacteria (SRB) develop syntrophic relationships anaerobic oxidizers (ANMEs) direct transfer or zero-valent sulphur, which would pull forward co-existence methanogens SRB middle deep layer sediments. Conclusions In addition offering perspective distribution genes/pathways, this study emphasizes role emissions various possible ANMEs The exploration provides novel insights into future synthetic microbial community construction analysis. This also has implications for predicting ecosystem functions within context environmental global change.

Language: Английский

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Microbial diversity and keystone species drive soil nutrient cycling and multifunctionality following mangrove restoration

Environmental Research, Journal Year: 2024, Volume and Issue: 251, P. 118715 - 118715

Published: March 14, 2024

Language: Английский

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Maize root-associated niches determine the response variation in bacterial community assembly and function to phthalate pollution

Journal of Hazardous Materials, Journal Year: 2022, Volume and Issue: 429, P. 128280 - 128280

Published: Jan. 19, 2022

Language: Английский

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A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities

Applied and Environmental Microbiology, Journal Year: 2022, Volume and Issue: 88(6)

Published: Feb. 9, 2022

Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in last decades. On other side, a synopsis culturable endophytic is still lacking literature.

Language: Английский

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

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(5), P. 1803 - 1823

Published: Jan. 26, 2022

Methane is a critical greenhouse gas with significant impacts on environmental and global change. However, CH4 cycling processes coupling mechanisms the biogeochemical of carbon, nitrogen, sulfur metals in environment remain elusive. To fill such knowledge gaps, we constructed manually curated methane database (MCycDB) for comprehensive accurate analysis microbial communities. MCycDB contains 298 gene families covering 10 metabolism pathways 610,208 representative sequences, associated reference sequences from NCBI RefSeq 48 phyla 2,197 genera, five 100 genera bacteria archaea, respectively. Also, homologous groups public orthology databases were identified included to reduce false positive assignments. We applied profile taxonomic various environments. Gene involved methanogenesis abundant hot spring sediment less freshwater, whereas ones aerobic oxidation permafrost peatland. This study demonstrates that useful tool studying microbially-driven high specificity, coverage accuracy.

Language: Английский

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The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

Environmental Microbiome, Journal Year: 2023, Volume and Issue: 18(1)

Published: June 1, 2023

Abstract Background Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, support existence multicellular life. The mangrove ecosystem is limited if not for microbial cycling nutrients, life this harsh environment would likely exist. mangroves Southeast Asia oldest most biodiverse on serve vital helping to prevent shoreline erosion, act as nursery grounds many marine species sequester carbon. Despite these recognised benefits importance microbes ecosystems, studies examining microbiome scarce.cxs Results Here we examine Avicenia alba Sonneratia identify a core 81 taxa. A further eight taxa ( Pleurocapsa , Tunicatimonas Halomonas Marinomonas Rubrivirga Altererythrobacte Lewinella, Erythrobacter ) were found be significantly enriched tree compartments suggesting key microbiome. majority those identified or production compounds that promote host survival. Conclusion identification furthers understanding biodiversity, particularly where such rare. different communities between sampling sites suggests environmental filtering occurring, with hosts selecting consortia suitable survival their immediate environment. As climate change advances, predicted change, however, without knowing what currently there, it impossible determine magnitude any deviations. This work provides an important baseline against which community can measured.

Language: Английский

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The Microbial Ecology of Estuarine Ecosystems

Annual Review of Marine Science, Journal Year: 2023, Volume and Issue: 16(1), P. 335 - 360

Published: July 7, 2023

Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These include high rates of primary production that nourish harvests commercially valuable species through fisheries aquaculture, the transformation terrestrial anthropogenic materials to help ensure water quality necessary support recreation tourism, mutualisms maintain blue carbon accumulation storage. Research ecology underlies in estuaries has expanded greatly across a range environments, including water, sediment, biofilms, biological reefs, stands seagrasses, marshes, mangroves. Moreover, application new molecular tools improved our understanding diversity genomic functions microbes. This review synthesizes recent research habitats contributions microbes food webs, elemental cycling, interactions with plants animals, highlights novel insights advances genomics.

Language: Английский

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Dynamic metabolites: A bridge between plants and microbes

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 899, P. 165612 - 165612

Published: July 20, 2023

Language: Английский

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Biochemical and multi-omics analyses of response mechanisms of rhizobacteria to long-term copper and salt stress: Effect on soil physicochemical properties and growth of Avicennia marina

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 466, P. 133601 - 133601

Published: Jan. 24, 2024

Language: Английский

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