Responses of soil micro-eukaryotic communities to decadal drainage in a Siberian wet tussock tundra.

Climate warming holds the potential to cause extensive drying of wetlands in the Arctic, but the warming-drying effects on belowground ecosystems, particularly micro-eukaryotes, remain poorly understood. We investigated the responses of soil micro-eukaryotic communities, including fungi, protists, and microbial metazoa, to decadal drainage manipulation in a Siberian wet tundra using both amplicon and shotgun metagenomic sequencing. Our results indicate that drainage treatment increased the abundance of both fungal and non-fungal micro-eukaryotic communities, with key groups such as Ascomycota (mostly order Helotiales), Nematoda, and Tardigrada being notably abundant in drained sites. Functional traits analysis showed an increase in litter saprotrophic fungi and protistan consumers, indicating their increased activities in drained sites. The effects of drainage were more pronounced in the surface soil layer than the deeper layer, as soils dry and warm from the surface. Marked compositional shifts were observed for both communities, with fungal communities being more strongly influenced by drainage-induced vegetation change than the lowered water table itself, while the vegetation effect on non-fungal micro-eukaryotes was moderate. These findings provide insights into how belowground micro-eukaryotic communities respond to the widespread drying of wetlands in the Arctic and improve our predictive understanding of future ecosystem changes.

Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages.

Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.

Disproportionate microbial responses to decadal drainage on a Siberian floodplain.

Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO2 and CH4 flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO2 and CH4 fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO2 emission rates and highly reduced CH4 emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.

Segregation of age-related skin microbiome characteristics by functionality.

Although physiological changes are the most evident indicators of skin aging by alteration of the skin's structure and function, we question whether skin aging is also affected by the structure and assembly process of the skin microbiome. We analysed the skin microbiomes of 73 healthy Chinese women in two age groups (25-35 years old and 56-63 years old) using 16S rRNA gene amplicon sequencing; the overall microbiome structure was significantly different between the two age groups. An analysis using ecological theory to evaluate the process of microbial community assembly processes revealed that the microbiomes of the older group were formed under a greater influence of the niche-based process, with the network of microbes being more collapsed than that of the younger group. Inferred metagenomic functional pathways associated with replication and repair were relatively more predominant in the younger group whereas, among the various metabolism-related pathways, those associated with biodegradation were more predominant in the older group. Interestingly, we found two segregated sub-typing patterns in the younger group which were also observed in the skin microbiomes of young Chinese women living in four other cities in China. The results of our study highlights candidate microbes and functional pathways that are important for future research into preventing skin aging and which could lead to a comprehensive understanding of age-related skin microbiome characteristics.

Fragile skin microbiomes in megacities are assembled by a predominantly niche-based process.

Given the higher incidence of skin diseases in more urbanized populations and its association with the skin microbiome, we questioned how the skin microbiome differed depending on the degree of urbanization. Skin microbiomes of 231 healthy subjects in five large cities in China varied mainly with environment and socioeconomic status of the cities in question. The differences among microbiomes could be explained by the predominantly niche-based assembly of microbial communities, which was supported by a dominance test, ß-null deviation, and edge-length abundance distribution. Networks among microbes in larger cities were more fragile, which may contribute to the higher incidence of skin diseases in more urbanized environments. These results suggest that microbial ecological theory can provide a framework for understanding crucial health-associated features of the human microbiome.

Collapse of human scalp microbiome network in dandruff and seborrhoeic dermatitis.

We investigate the relationship between scalp microbiota and dandruff/seborrhoeic dermatitis (D/SD), an unpleasant scalp disorder common in human populations. Bacterial and fungal community analyses on scalp of 102 Korean were performed by next-generation sequencing. Overall scalp microbiome composition significantly differed between normal and disease groups, and especially co-occurrence network of dominant members was breakdown in disease groups. These findings will provide novel insights into shifts of microbial community relevant to D/SD.

Complete genome sequence of antibiotic and anticancer agent violacein producing Massilia sp. strain NR 4-1.

Massilia sp. NR 4-1 was a violacein producing strain newly isolated from topsoil under nutmeg tree, Torreya nucifera in Korean national monument Bijarim Forest. Violacein is a novel class of drug exhibiting anticancer and antibiotic activities originated from l-tryptophan. Here, we present the complete genome of Massilia sp. strain NR 4-1 of 6,361,416bp and total 5285 coding sequences (CDSs) including a complete violacein biosynthesis pathway, vioABCDE. The genome sequence of Massilia sp. NR 4-1 will provide stable and efficient biotechnological applications of violacein production.