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). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. RESULTS: In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. CONCLUSIONS: One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.

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). Compared with the untreated control areas (samples taken from the upper chest), treatment with Moisturizer K prevented a reduction in bacterial and fungal richness, and increased the change ratio of the relative abundance of commensal bacteria, such as Staphylococcus epidermidis and Ralstonia, at the treated sites (samples taken from the forehead). Moreover, Moisturizer K-treated ex vivo skin explants had higher levels of caspase 14 (a marker of skin barrier function), collagen I, and elastin (structure components), and lower levels of aryl hydrocarbon receptor (AHR; activated by air pollutants) and interleukin-6 (IL-6) than those in explants treated with other moisturizers and in the untreated areas of the skin. These results suggest that a skin postbiotic moisturizer with yeast extract supports the regulation of the skin's microbiome balance and may provide a holistic barrier (involving skin microbiome, physical, chemical, and immune barriers) to protect the skin against environmental aggressors.

Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae.

Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23T and J2-29T, showing catalase- and oxidase-positive activities were isolated from species of the marine algae Chondrus and Ulva, respectively. Both strains optimally grew at 30 °C, pH 7.0 and 2% (w/v) NaCl. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain G2-23T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c) as major cellular fatty acids, and phosphatidylethanolamine (PE), phosphatidyl-N-monomethylethanolamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol and an unidentified phospholipid (PL) as major polar lipids. Strain J2-29T contained summed feature 8, C18 : 1 ω7c 11-methyl and C16 : 0 as major cellular fatty acids and PE, PME, PG and PL as major polar lipids. The genomic DNA G+C contents of strains G2-23T and J2-29T were 59.5 and 62.2 mol%, respectively. Both strains shared 97.9 % 16S rRNA gene sequence similarity, 79.8 % average nucleotide identity (ANI) and 22.8 % digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic and phylogenomic analyses by 16S rRNA gene and genome sequences, respectively, revealed that strains G2-23T and J2-29T formed different phylogenic lineages within the genus Hoeflea. ANI and dDDH values between strains G2-23T and J2-29T and other Hoeflea type strains were less than 79.0 and 22.1% and 80.5 and 23.3 %, respectively, suggesting that they represent novel species of the genus Hoeflea. In summary, based on their phenotypic, chemotaxonomic and molecular properties, strains G2-23T and J2-29T represent two different novel species of the genus Hoeflea, for which the names Hoeflea algicola sp. nov. (G2-23T=KACC 22714T=JCM 35548T) and Hoeflea ulvae sp. nov. (J2-29T=KACC 22715T=JCM 35549T), respectively, are proposed.

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

The newly discovered complete ammonia-oxidizing (comammox) Nitrospira 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 Nitrospira, 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 Nitrospira was more sensitive to increased salinity than that of other ammonia oxidizers. The results obtained with DNA-SIP heavy fractions showed that the dominant phylotype in clade A.2 (containing genes involved in the adaptation to haloalkaline environments) had high proportions in comammox Nitrospira community under both freshwater (0.06% salinity) and highly saline water (3% salinity) conditions. In contrast, another phylotype of clade A.2 (which lacks these genes) was dominant only under freshwater conditions. The PARs confirmed that comammox Nitrospira presented greater contributions to nitrification under freshwater conditions with a PAR of 4.37 ± 0.53 mg N·day-1·kg soil-1 (54%) than under saline water conditions with a PAR of 0.60 ± 0.94 mg N·day-1·kg soil-1 (18%). Moreover, AOA were specific to saline water conditions, whereas AOB were common under both freshwater and saline water conditions (44% and 52%, respectively). The present study provided evidence that salinity markedly affects the activity of comammox Nitrospira, and that the salt sensitivity of different phylotypes varies. IMPORTANCE Complete ammonia oxidation (comammox) is a newly discovered type of nitrification through which ammonia is oxidized to nitrate in an organism. Comammox Nitrospira were abundantly found in coastal ecosystems and demonstrated high community diversity. Changes in salinity are considered one of the most important factors to comammox Nitrospira in coastal ecosystems; however, reports on the correlation between them remain inconsistent. Therefore, it is critical to experimentally determine the influence of salinity on comammox Nitrospira in the coastal ecosystem. This study demonstrated a clear effect of salinity on the abundance, activity, and relative contribution of different ammonia oxidizers, especially for comammox Nitrospira. To the best of our knowledge, this is the first study demonstrating comammox Nitrospira activity at seawater salinities, implying the existence of a salt-tolerant type comammox Nitrospira, despite its activity being much lower than in freshwater conditions. The indicated correlation between the activity of specific comammox Nitrospira and salinity is anticipated to provide insights into the distribution of comammox Nitrospira and their potential contributions in estuaries and coastal ecosystems.

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

A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558T, was isolated from sediment sampled in the Mariana Trench. Strain 960558T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558T is Planktotalea lamellibrachiae JAM 119T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C16 : 0, 11-methyl C18 : 1 ω7c and C18 : 1 ω7c and/or C18 : 1 ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558T (=KCTC 82619T=MCCC 1K04727T).

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. Compared with that of the vaginally born children, the skin mycobiome of caesarean-born children is assembled by predominantly deterministic niche-based processes and exhibits a more fragile microbial network at all three sampling sites. Moreover, vaginal delivery leads to clearer intra- and interindividual specialization of fungal structures with increasing age; this phenomenon is not observed in caesarean-born children. The maternal correlation with children also differs based on the mode of delivery; specifically, the mycobiomes of vaginally born children at younger ages are more strongly correlated with vagina-associated fungal genera (Candida and Rhodotorula), whereas those of caesarean-delivered children at elder age include more skin-associated and airborne fungal genera (Malassezia and Alternaria). Based on this ecological framework, our results suggest that the delivery mode is significantly associated with maturation of the skin fungal community in children. IMPORTANCE Human skin is permanently colonized by microbes starting at birth. The hygiene hypothesis suggests that a lack of early-life immune imprinting weakens the body's resilience against atopic disorders later in life. To better understand fungal colonization following early-life periods affected by interruption, we studied the skin mycobiomes of 73 children and their mothers. Our results suggest a differentiation of the skin mycobiomes between caesarean-born and vaginally born children. Caesarean-born children exhibit a mycobiome structure with more fitted deterministic niche-based processes, a fragile network, and an unchanged microbial dissimilarity over time. In vaginally born children, this dissimilarity increases with age. The results indicate that initial microbial colonization has a long-term impact on a child's skin mycobiome. We believe that these findings will inspire further investigations of the "hygiene hypothesis" in the human microbiome, especially in providing novel insights into influences on the development of the early-life microbiome.

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. In the activated sludges in the WWTPs, comammox clade A.1 was widely distributed and mostly comprised Candidatus Nitrospira nitrosa-like comammox (>98% of all comammox). The proportion of this clade was negatively correlated (p < 0.01) with the dissolved oxygen (DO) level (1.7−8 mg/L), and slight pH changes (7.20−7.70) affected the structure of the comammox populations. Nitrospira lineage I frequently coexisted with Nitrosomonas, which generally had a significant positive correlation (p < 0.05) with the DO level. Our study provided an insight into the structure of comammox and other nitrifier populations in WWTPs that use the anaerobic−anoxic−aerobic process, broadening the knowledge about the effects of DO on comammox and other nitrifiers.

Methylophaga pinxianii sp. nov., isolated from the Mariana Trench.

Two strains, TMB456T 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 Methylophaga of the class Gammaproteobacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Methylophaga muralis Kr3T (98.1 % similarity) and Methylophaga nitratireducenticrescens JAM1T (97.3 % similarity). Digital DNA-DNA hybridization values of TMB456T with M. muralis Kr3T and M. nitratireducenticrescens JAM1T were <25 %. The average nucleotide identity value between strain TMB456T and M. muralis Kr3T was 80.9 %. The genomic DNA G+C contents of strains TMB456T and TMB1265 were both 44.9 mol %. Strains TMB456T and TMB1265 could grow at 4-37 °C (optimum at 20-28 °C), at pH 3-10 (optimum at pH 7-9) and in the presence of 0-10 % (w/v) NaCl (optimum at 0-1 %). Cells of strains TMB456T and TMB1265 were Gram-negative rods (0.3-0.6 µm×0.7-1.3 µm). Chemotaxonomic analysis showed that ubiquinone 8 was the sole quinone produced by strain TMB456T and that the major cellular fatty acids were iso-C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile of this strain included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipids and two unidentified polar lipids. Based on the phenotypic, chemotaxonomic and molecular features, strains TMB456T and TMB1265 belong to a novel species within the genus Methylophaga, for which the name Methylophaga pinxianii sp. nov. is proposed. The type strain is TMB456T (=KCTC 82622T= MCCC 1K05898T).

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

Two strains, TMPB967T and TTPB476, were isolated from two different locations in the Mariana Trench. Cells of strains TMPB967T and TTPB476 were Gram-negative, curved rod-shaped (0.35-0.6 µm×2-4 µm) with flagella. Both strains were catalase- and oxidase-positive. Strains TMPB967T and TTPB476 could grow at 4-37 °C (optimum, 37 °C), at pH 6-9 (optimum, pH 6-7) and in the presence of 0-8 % (w/v) NaCl (optimum, 5 %). Both strains could grow with tetradecane or hexadecane as the sole carbon source. The predominant isoprenoid quinone was ubiquinone 9. The major cellular fatty acids of strains TMPB967T and TTPB476 were C18 : 1 ω9c, C16 : 0 and summed feature 3 (C16 : 1 ω7c or ω6c). The polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminolipid. The DNA G+C contents of strains TMPB967T and TTPB476 were 53.1 and 53.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Thalassolituus marinus IMCC1826T (97.1 % similarity) and Thalassolituus oleivorans MIL-1T (95.9 % similarity). Digital DNA-DNA hybridization results of strain TMPB967T with TTPB476, T. marinus IMCC1826T and T. oleivorans MIL-1T were 99.9, 20.9 and 20.2 %, respectively. Average nucleotide identity results of strain TMPB967T with TTPB476, T. marinus IMCC1826T and T. oleivorans MIL-1T were 100, 75.8 and 72.0 %, respectively. On the basis of the phenotypic, chemotaxonomic and molecular features, strains TMPB967T and TTPB476 belong to a novel species within the genus Thalassolituus, for which the name Thalassolituus alkanivorans sp. nov. is proposed. The type strain is TMPB967T (=KCTC 82621T=MCCC 1K05476T).

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. Plants of angiosperms, gymnosperms, and pteridophytes were involved. Plant taxonomy, leaf side, growing environment, and evolutionary relationships were considered. We found that pteridophytes showed the higher fungal species diversity, stronger mutualistic fungal interactions, and a greater percentage of putative pathogens than gymnosperms and angiosperms. Plant taxonomic group, leaf side, and growing environment were significantly associated with the foliar epiphytic mycobiome, but the similarity of the mycobiomes among plants was not directly related to the distance of the host evolutionary tree. Our results provide a general understanding of the foliar fungal mycobiomes from pteridophytes to angiosperms. These findings will facilitate our understanding of foliar fungal epiphytes and their roles in plant communities and ecosystems.

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. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 µmol/g d.w.s (µmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.

Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Rhodococcus 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 Rhodococcus 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 Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear megaplasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated the mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient Rhodococcus erythropolis strain in a mating experiment and showed similar ethane- and propane-consuming activities. Finally, our findings demonstrate that the horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. IMPORTANCE CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient similar abilities to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane degradation. Our results indicate that plasmids can support the rapid evolution of enzyme-mediated biogeochemical processes.

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. D7000 has a genome consisting of 4,558,742 bp, including one chromosome and nine plasmids. This strain exhibits extracellular protease activity under low temperatures. Among 4328 protein-coding sequences (CDSs), 47 encode serine peptidases. Multiple annotation analysis was used to identify two genes encoding extracellular subtilases. In addition, three types of extracellular secretion transporter systems were found upon pathway construction and analysis. Genome analysis offers insights into the putative pathway of extracellular protease and application prospect of Deinococcus sp. D7000 in enzyme development.

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. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.

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. Skin fungal diversity decreased after the first three months of life. Differences in fungal community composition were greater among individual infants than among the three skin sites in the same individual. Inter- and intra-individual variation were similar and lower, respectively, than the variability between two samples obtained 12 weeks apart, from the same site in the same subject, suggesting low stability of fungal communities on infant skin. Skin physiological parameters showed little correlation with skin fungal community structure. Additionally, Malassezia was the most represented genus (36.43%) and M. globosa was the most abundant species in Malassezia with its abundance decreasing from 54.06% at 0-2 months to 34.54% at 5-6 months. These findings provide a basis for investigating the causative fungi-skin interactions associated with skin diseases.

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

Complete ammonia-oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus Nitrospira, which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from that of comammox Nitrospira has become problematic, since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox Nitrospira clade A- and B-specific primer sets targeting the α-subunit of the ammonia monooxygenase gene (amoA) and a sNOB-specific primer set targeting the cyanase gene (cynS) for quantitative PCR (qPCR). The high coverage and specificity of these primers were checked by use of metagenome and metatranscriptome data sets. Efficient and specific amplification with these primers was demonstrated using various environmental samples. Using the newly designed primers, we successfully estimated the abundances of comammox Nitrospira and sNOB in samples from two chloramination-treated drinking water systems and found that, in most samples, comammox Nitrospira clade A was the dominant type of Nitrospira and also served as the primary ammonia oxidizer. Compared with other ammonia oxidizers, comammox Nitrospira had a higher abundance in process water samples in these two drinking water systems. We also demonstrated that sNOB can be readily misrepresented by an earlier method, calculated by subtracting the comammox Nitrospira abundance from the total Nitrospira abundance, especially when the comammox Nitrospira proportion is relatively high. The new primer sets were successfully applied to comammox Nitrospira and sNOB quantification, which may prove useful in understanding the roles of Nitrospira in nitrification in various ecosystems.IMPORTANCENitrospira is a dominant nitrite-oxidizing bacterium in many artificial and natural environments. The discovery of complete ammonia oxidizers in the genus Nitrospira prevents the use of previously identified primers targeting the Nitrospira 16S rRNA gene or nitrite oxidoreductase (nxr) gene for differential determination of strict nitrite-oxidizing bacteria (sNOB) in the genus Nitrospira and among comammox bacteria in this genus. We designed three novel primer sets that enabled quantification of comammox Nitrospira clades A and B and sNOB with high coverage, specificity, and accuracy in various environments. With the designed primer sets, sNOB and comammox Nitrospira were differentially estimated in drinking water systems, and we found that comammox clade A predominated over sNOB and other ammonia oxidizers in process water samples. Accurate quantification of comammox Nitrospira and sNOB by use of the newly designed primers will provide essential information for evaluating the contribution of Nitrospira to nitrification in various ecosystems.

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. METHODS: Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status. RESULTS: Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples. CONCLUSION: We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.

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. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.

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. Relative abundances of Streptococcus and Granulicatella were negatively correlated with age, and the alpha diversity at all body sites examined increased during the first 10 years of life, especially on the face. The facial bacterial composition of 10-year-old children was strongly associated with delivery mode at birth. Among mother-child pairs (50 pairs), the relative abundances of most bacterial genera in children were more similar to those of their own mothers than those of unrelated women. The data indicated that age and site were significantly associated with microbial composition and that maternal factors determine the child's microbiome. Further research is needed to characterize the effects of maturation of the infant microbiome on health in adulthood.

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

A Gram-stain-negative, strictly aerobic bacterium, designated StC1T, 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 StC1T was observed at 30-45 °C(optimum, 37 °C), pH 6.0-11.0 (pH 7.0) and in the presence of 1.0-8.0 % (w/v) NaCl (2 %). Strain StC1T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1 ω6c) and 11-methyl-C18 : 1ω7c as the major fatty acids. Sulfoquinovosyl diacylglycerol, phosphatidylethanolamine and phosphatidylglycerol and ubiquinone-10 were identified as the major polar lipids and the sole isoprenoid quinone, respectively. The G+C content of the genomic DNA was 64.7 mol%. Strain StC1T was most closely related to Oricola cellulosilytica CC-AMH-OT, Nitratireductor basaltis J3T, Aquamicrobiumahrensii 905/1T and Mesorhizobium tamadayense Ala-3T with 97.3 , 96.9 , 96.8  and 96.6 % 16S rRNA gene sequence similarities, respectively, but it formed a distinct phylogenic lineage within the family Phyllobacteriaceae. On the basis of phenotypic, chemotaxonomic and molecular properties, strain StC1T represents a novel genus of the family Phyllobacteriaceae, for which the name Oceaniradius stylonematis gen. nov., sp. nov. is proposed. The type strain is StC1T (=KACC 19231T=JCM 32050T).