Genome sequence of HH-03 isolated from dairy pipeline.

In this study, HH-03 was isolated from a dairy pipeline, and its genomic information was obtained by performing sequencing. The genome size of strain HH-03 was 3.85 Mbp with a GC content of 41.

Abundance and distribution of complete ammonia oxidizers under a salinity gradient in the Yangtze Estuary and its adjacent sea.

Aims: This study investigated the distribution, community composition, and environmental drivers of complete ammonia-oxidizing bacteria (comammox) in estuarine sediments, focusing on the Yangtze River Estuary. It examined how environmental gradients-particularly salinity, pH, and ammonium concentration-influence comammox abundance and diversity, thereby clarifying their ecological niche in transitional aquatic ecosystems.

Methods And Results: Seventeen sediment samples were collected across the estuary.

". Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres.

Unlabelled: Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper ( L.) and ginseng plants ( C.

Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment.

Background: The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA).

Effects of Investigational Moisturizers on the Skin Barrier and Microbiome following Exposure to Environmental Aggressors: A Randomized Clinical Trial and Ex Vivo Analysis.

The skin microbiota barrier participates in skin barrier function in addition to the physical, chemical, and immunological protective barriers, and is affected by environmental aggressors and skincare regimens. To better understand the exact effects of real-life environmental conditions on the skin and determine the protective methods, this study investigates the effects of three topical cosmetic moisturizers (water gel moisturizers with/without yeast extract (Moisturizers K and C) and a thick-emulsion cream moisturizer (Moisturizer L)) on clinical and skin microbiome endpoints in the presence of environmental aggressors during an 8-week, randomized controlled, triple-blind clinical trial with 110 participants, and molecular- as well as biomarker-level endpoints on ex vivo skin explants after exposure to simulate urban environmental conditions. The results show that all moisturizers are well-tolerated and improve skin barrier function and surface moisture content from the baseline, and the improvement is maintained at the last analysis point (3 days after trial completion).

sp. nov. and sp. nov., isolated from phycosphere of marine algae.

Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23 and J2-29, showing catalase- and oxidase-positive activities were isolated from species of the marine algae and , respectively. Both strains optimally grew at 30 °C, pH 7.0 and 2% (w/v) NaCl.

Salinity changes the nitrification activity and community composition of comammox in intertidal sediments of Yangtze River estuary.

The newly discovered complete ammonia-oxidizing (comammox) has been identified in different environments, including coastal environments, where salinity is one of the most important factors for the abundance and activity of nitrifiers. Here, we demonstrate the effect of salinity on comammox , canonical ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in the intertidal sediments of the Yangtze River estuary based on microcosm experiments, DNA stable-isotope probing (DNA-SIP), and potential ammonium-oxidation rate (PAR) tests for different groups of ammonia oxidizers with selective inhibitors. During microcosm incubations, the abundance of comammox was more sensitive to increased salinity than that of other ammonia oxidizers.

gen. nov., sp. nov., a novel member of the family , isolated from the Mariana Trench.

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.

Infant Mode of Delivery Shapes the Skin Mycobiome of Prepubescent Children.

Characterizing the skin mycobiome is necessary to define its association with the host immune system, particularly in children. In this study, we describe the skin mycobiome on the face, ventral forearm, and calf of 72 prepubescent children (aged 1 to 10 years) and their mothers, based on internal transcribed spacer (ITS) amplicon sequencing. The age and delivery mode at birth are the most influential factors shaping the skin mycobiome.

Abundance and Niche Differentiation of Comammox in the Sludges of Wastewater Treatment Plants That Use the Anaerobic-Anoxic-Aerobic Process.

Complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate, were recently identified and found to be ubiquitous in artificial systems. Research on the abundance and niche differentiation of comammox in the sludges of wastewater treatment plants (WWTPs) would be useful for improving the nitrogen removal efficiency of WWTPs. Here, we investigated the relative abundance and diversity of comammox in fifteen sludges of five WWTPs that use the anaerobic−anoxic−aerobic process in Jinan, China, via quantitative polymerase chain reaction and high-throughput sequencing of the 16S rRNA gene and ammonia monooxygenase gene.

sp. nov., isolated from the Mariana Trench.

Two strains, TMB456 and TMB1265, were isolated from different locations in the Mariana Trench. Analysis of the 16S rRNA gene and genomic rRNA sequences indicated that they were from the same novel species and were affiliated with the genus of the class . Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Kr3 (98.

sp. nov., a hydrocarbon-utilizing bacterium isolated from the Mariana Trench.

Two strains, TMPB967 and TTPB476, were isolated from two different locations in the Mariana Trench. Cells of strains TMPB967 and TTPB476 were Gram-negative, curved rod-shaped (0.35-0.

Cross-phytogroup assessment of foliar epiphytic mycobiomes.

The foliar surface forms one of the largest aboveground habitats on Earth and maintains plant-fungus relationships that greatly affect ecosystem functioning. Despite many studies with particular plant species, the foliar epiphytic mycobiome has not been studied across a large number of plant species from different taxa. Using high-throughput sequencing, we assessed epiphytic mycobiomes on leaf surfaces of 592 plant species in a botanical garden.

Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary.

Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained.

Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Bacteria.

The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are involved not only in methane oxidation but also in short-chain alkane oxidation. Here, we describe sp. strain ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source, and report on the horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMOs) of the CuMMO family and the sMMO (soluble methane monooxygenase)-like SDIMO in the genus .

The complete genome of extracellular protease-producing Deinococcus sp. D7000 isolated from the hadal region of Mariana Trench Challenger Deep.

The general features and genomic characteristics of gram-positive Deinococcus sp. D7000 isolated from the hadal region of Mariana Trench Challenger Deep were analyzed in this study. Deinococcus sp.

Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants.

The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China.

Dynamics of Skin Mycobiome in Infants.

Understanding the microbial community structure of the human skin is important for treating cutaneous diseases; however, little is known regarding skin fungal communities (mycobiomes). The aim of the present study was to investigate the features of and variations in skin fungal communities during infancy in 110 subjects less than 6 months of age. Skin samples were obtained from the back, antecubital fossa, and volar forearm, while physiological parameters including transepidermal water loss, pH, surface moisture, and deep layer hydration were evaluated.

Use of Newly Designed Primers for Quantification of Complete Ammonia-Oxidizing (Comammox) Bacterial Clades and Strict Nitrite Oxidizers in the Genus .

Complete ammonia-oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus , which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from that of comammox has become problematic, since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox clade A- and B-specific primer sets targeting the α-subunit of the ammonia monooxygenase gene () and a sNOB-specific primer set targeting the cyanase gene () for quantitative PCR (qPCR).

Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.

Background: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets.

Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.

Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain.

Age and Mothers: Potent Influences of Children's Skin Microbiota.

The evolution of a child's skin microbiome is associated with the development of the immune system and skin environment. As only few studies have analyzed the microbiota in young children, we investigated changes in the skin microbiota of children (158 subjects; ≤10 years old) and compared the microbiota structures between children and their mothers using 16S rRNA gene amplicon sequencing. Sample location and age were the primary factors determining a child's skin bacterial composition, which differed significantly among the face, ventral forearm, and calf.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments.

Oceaniradius stylonematis gen. nov., sp. nov., isolated from a red alga, Stylonema cornu-cervi.

A Gram-stain-negative, strictly aerobic bacterium, designated StC1, was isolated from a marine alga, Stylonema cornu-cervi, in the Republic of Korea. Cells were oxidase- and catalase-positive rods that were motile by a single lateral flagellum. Growth of strain StC1 was observed at 30-45 °C(optimum, 37 °C), pH 6.

Rhodophyticola porphyridii gen. nov., sp. nov., isolated from a red alga, Porphyridium marinum.

A Gram-stain-negative, strictly aerobic and moderately halophilic bacterium, designated strain MA-7-27, was isolated from a marine red alga, Porphyridium marinum, in the Republic of Korea. The cells of strain MA-7-27 were non-motile rods showing oxidase- and catalase-positive activities. Growth of strain MA-7-27 was observed at 15-45 °C (optimum, 30 °C), pH 5.