". 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.

Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project.

Unlabelled: The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results.

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.

Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions.

The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics.

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.

Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism.

The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)).

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.

Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata.

The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient.

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).

Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China.

Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China.