Key bacteria decomposing animal and plant detritus in deep sea revealed via long-term incubation in different oceanic areas.

Transport of organic matter (OM) occurs widely in the form of animal and plant detritus in global oceans, playing a crucial role in global carbon cycling. While wood- and whale-falls have been extensively studied, the process of OM remineralization by microorganisms remains poorly understood particularly in pelagic regions on a global scale. Here, enrichment experiments with animal tissue or plant detritus were carried out in three deep seas for 4-12 months using the deep-sea incubators.

New Phthalides and Isochromanone Derivatives from the Deep-Sea-Derived Fungus Penicillium bialowiezense A3.

Two new phthalide derivatives, namely bialowalides A (1) and B (8), and one new isochromanone analogue biourgalide C (11), together with 8 known phthalides (2-7, 9, and 10) as well as two known isochromanones (12 and 13) were discovered from the EtOAc extract of the deep-sea-derived fungus Penicillium bialowiezense A3. The structures were resolved on the basis of extensive spectroscopic analyses (NMR and HRESIMS data), in association with the modified Mosher's method and ECD data for the determination of the absolute configurations. All isolated secondary metabolites (1-13) were tested their antiviral activities against the SARS-CoV-2 trVLP pseudovirus at a concentration of 25 μM.

Polyethylene terephthalate (PET)-degrading bacteria in the pelagic deep-sea sediments of the Pacific Ocean.

Polyethylene terephthalate (PET) plastic pollution is widely found in deep-sea sediments. Despite being an international environmental issue, it remains unclear whether PET can be degraded through bioremediation in the deep sea. Pelagic sediments obtained from 19 sites across a wide geographic range in the Pacific Ocean were used to screen for bacteria with PET degrading potential.

The Effects and Toxicity of Different Pyrene Concentrations on Using Transcriptomic Analysis.

Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in under different pyrene concentrations using transcriptome sequencing technology.

sp. nov., isolated from the seawater of Dongshan Island.

A taxonomic study was carried out on strain yzlin-01, isolated from Dongshan Island seawater. The bacterium was Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, and motile by polar flagella. Growth was observed at temperatures of 10-40 °C, at salinities of 0.

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary.

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains).

Virus diversity and interactions with hosts in deep-sea hydrothermal vents.

Background: The deep sea harbors many viruses, yet their diversity and interactions with hosts in hydrothermal ecosystems are largely unknown. Here, we analyzed the viral composition, distribution, host preference, and metabolic potential in different habitats of global hydrothermal vents, including vent plumes, background seawater, diffuse fluids, and sediments.

Results: From 34 samples collected at eight vent sites, a total of 4662 viral populations (vOTUs) were recovered from the metagenome assemblies, encompassing diverse phylogenetic groups and defining many novel lineages.

Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope.

A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea.

sp. nov., a moderate halophile isolated from hypersaline sediments of the Qaidam Basin in Northwest China.

A Gram-stain-positive, moderately halophilic, aerobic, endospore-forming, rod-shaped bacterium, designated strain DP4-553-S, was isolated from hypersaline sediment collected from the Dalangtan Playa in the Qaidam Basin, Northwest PR China. Growth occurred within 0-21.6% (w/v) NaCl (optimum 7.

Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China.

Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China.

Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome.

Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations.

Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation.

Background: Members of the group (abbreviated as the group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation.

Spatiotemporal Dynamics of Communities and Abundance in Dongshan Bay, South of China.

The genus inhabit estuarine and marine ecosystem throughout the world and can cause severe infections in humans and animals. Previous studies have demonstrated the dynamics of at both community and population levels and assessed the close relationship between environmental factors and diversity and abundance, such as temperature, salinity, and dissolved oxygen. It is also generally believed that aquaculture is the fastest-growing food sector, which is also applying great environmental impacts on microbial communities in aquatic ecosystems.

Distribution of Bathyarchaeota Communities Across Different Terrestrial Settings and Their Potential Ecological Functions.

High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database. In total, 1456 Bathyarchaeota sequences from 28 sites were subjected to UniFrac analysis based on phylogenetic distance and multivariate regression tree analysis of taxonomy.

Modeling single-vehicle run-off-road crash severity in rural areas: Accounting for unobserved heterogeneity and age difference.

This study investigates factors that significantly contribute to the severity of driver injuries resulting from single-vehicle run-off-road (SV ROR) crashes. A mixed logit model approach is employed to explore the potential unobserved heterogeneous effects associated with each age group: young (ages 16-24), middle-aged (ages 25-65), and older drivers (ages over 65). Likelihood ratio tests indicated that the development of separate injury severity models for each age group is statistically superior to estimating a single model using all data.

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China.

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences.

Inhibition of bacterial oxidation of ferrous iron by lead nitrate in sulfate-rich systems.

Inhibition of bacterial oxidation of ferrous iron (Fe(II)) by Pb(NO(3))(2) was investigated with a mixed culture of Acidithiobacillus ferrooxidans. The culture was incubated at 30 °C in ferrous-sulfate medium amended with 0-24.2 mM Pb(II) added as Pb(NO(3))(2).