Publications by authors named "Dayu Zou"

Background: Myxococcota, characterized by their distinct social lifestyles, are widely distributed micro-predators in global sediments. They can feed on a wide range of bacterial, archaeal, and fungal prey. Myxococcota are capable of producing diverse secondary metabolites, playing key roles in microbial food webs, and regulating the microbial community structures in different ecosystems.

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  • Land-ocean interactions play a crucial role in the evolution of coastal life, particularly for microorganisms in brackish waters, which remain largely unexplored.
  • This study focuses on the heterotrophic archaea Poseidoniales and reveals that their brackish subgroups originated over 600 million years ago due to a genetic adaptation that allowed them to tolerate osmotic stress.
  • Findings suggest that a spike in evolutionary rates occurred during the Cryogenian Snowball Earth event, potentially driven by increased phosphorus and algae, emphasizing the link between genetic changes and ecosystem evolution that set the stage for the Cambrian explosion of animals.
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  • Ammonia-oxidizing archaea (AOA) are crucial in nitrogen and carbon cycling, particularly in estuarine environments, but their genomic traits and ecological niches are not well understood.
  • Through metagenomic analysis of three Chinese estuaries, researchers found that AOA were the main ammonia oxidizers, identifying five major AOA groups.
  • The study revealed that AOA communities are influenced by spatial and environmental factors, with estuarine AOA exhibiting unique genomic features that aid their adaptation to high salinity conditions.
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Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118, the first cultured representative of a previously uncultivated order UBA8317 within , based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses.

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Background: The metabolic interactions of microbes significantly affect the assembly of microbial communities that play important roles in biogeochemical processes. However, most interspecies interactions between microorganisms in natural communities remain unknown, leading to a poor understanding of community assembly mechanisms.

Results: Here, we used a genome-scale metabolic modeling-based approach to explore the potential interactions among bacteria and archaea in mangrove sediments.

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Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences.

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Water hypoxia (DO < 2 mg/L) is a growing global environmental concern that has the potential to significantly influence not only the aquatic ecosystem but also the benthic sedimentary ecosystem. The Changjiang River Estuary hypoxia, classified as one of the world's largest seasonal hypoxic water basins, has been reported to be expanding rapidly in recent decades. However, the microbial community dynamics and responses to this water hypoxia are still unclear.

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  • The study explores the community composition of complete ammonia oxidizers (comammox) in the Pearl River Estuary (PRE) along a salinity gradient, revealing high diversity and distinct distribution patterns between upstream and downstream habitats.
  • Quantitative PCR results show that comammox microorganisms dominate upstream sediments, while ammonia-oxidizing archaea (AOA) are more prevalent downstream, with ammonia-oxidizing bacteria (AOB) being less significant overall.
  • The findings indicate that deterministic processes related to environmental factors like salinity and total nitrogen are more influential than stochastic processes in shaping the comammox community assembly from freshwater to marine environments.
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  • The archaeal phylum Woesearchaeota, part of the DPANN superphylum, consists of diverse microorganisms whose biology remains largely unstudied due to a scarcity of cultured isolates.
  • Current research involves analyzing 16S rRNA gene sequences and metagenome-assembled genomes to explore the global distribution, ecological preferences, and possible metabolic abilities of these organisms.
  • Phylogenomic findings classify Woesearchaeota into ten subgroups, with most expected to lead a symbiotic lifestyle, while subgroup J may live independently, and their genomes suggest potential metabolic roles as anaerobic fermentative heterotrophs.
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Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community.

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Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China.

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, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Metabolic pathways of the members are diverse and, hence, this phylum has been proposed to play an important role in global biogeochemical cycles. members are distributed in the estuarine environments.

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Ammonia-oxidizing archaea (AOA) are ubiquitous in natural ecosystems, and they are responsible for a significant fraction of ammonia oxidation globally. Since the first AOA isolate was established a decade ago, molecular surveys of their environmental distribution [based primarily on amplicon sequencing of the amoA, which codes for the alpha subunit of ammonia monooxygenase (AMO)], show that their habitats are believed to range from marine to terrestrial environments. However, the mechanisms of adaptation underpinning to their habitat expansion remain poorly understood.

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