Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class Ktedonobacteria

Soil microbial sensitivity to temperature remains unchanged despite community compositional shifts along geothermal gradients

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon-climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long-term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long-term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade-offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0-50 and 50-100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q₁₀ ). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long-term warming selects for warm-adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long-term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon-climate feedback projections.

Microbiological and Nutritional Analysis of Lettuce Crops Grown on the International Space Station

The ability to grow safe, fresh food to supplement packaged foods of astronauts in space has been an important goal for NASA. Food crops grown in space experience different environmental conditions than plants grown on Earth (e.g., reduced gravity, elevated radiation levels). To study the effects of space conditions, red romaine lettuce, Lactuca sativa cv 'Outredgeous,' plants were grown in Veggie plant growth chambers on the International Space Station (ISS) and compared with ground-grown plants. Multiple plantings were grown on ISS and harvested using either a single, final harvest, or sequential harvests in which several mature leaves were removed from the plants at weekly intervals. Ground controls were grown simultaneously with a 24-72 h delay using ISS environmental data. Food safety of the plants was determined by heterotrophic plate counts for bacteria and fungi, as well as isolate identification using samples taken from the leaves and roots. Molecular characterization was conducted using Next Generation Sequencing (NGS) to provide taxonomic composition and phylogenetic structure of the community. Leaves were also analyzed for elemental composition, as well as levels of phenolics, anthocyanins, and Oxygen Radical Absorbance Capacity (ORAC). Comparison of flight and ground tissues showed some differences in total counts for bacteria and yeast/molds (2.14 - 4.86 log10 CFU/g), while screening for select human pathogens yielded negative results. Bacterial and fungal isolate identification and community characterization indicated variation in the diversity of genera between leaf and root tissue with diversity being higher in root tissue, and included differences in the dominant genera. The only difference between ground and flight experiments was seen in the third experiment, VEG-03A, with significant differences in the genera from leaf tissue. Flight and ground tissue showed differences in Fe, K, Na, P, S, and Zn content and total phenolic levels, but no differences in anthocyanin and ORAC levels. This study indicated that leafy vegetable crops can produce safe, edible, fresh food to supplement to the astronauts' diet, and provide baseline data for continual operation of the Veggie plant growth units on ISS.

Dictyobacter vulcani sp. nov., belonging to the class Ktedonobacteria, isolated from soil of the Mt Zao volcano

An aerobic, Gram-stain-positive, mesophilic Ktedonobacteria strain, W12T, was isolated from soil of the Mt Zao volcano in Miyagi, Japan. Cells were filamentous, non-motile, and grew at 20–37 °C (optimally at 30 °C), at pH 5.0–7.0 (optimally at pH 6.0) and with <2 % (w/v) NaCl on 10-fold diluted Reasoner’s 2A (R2A) medium. Oval-shaped spores were formed on aerial mycelia. Strain W12T hydrolysed microcrystalline cellulose and xylan very weakly, and used d-glucose as its sole carbon source. The major menaquinone was MK-9, and the major cellular fatty acids were C16 : 1 2-OH, iso-C17 : 0, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and anteiso-C17 : 0. Cell-wall sugars were mannose and xylose, and cell-wall amino acids were d-glutamic acid, glycine, l-serine, d-alanine, l-alanine, β-alanine and l-ornithine. Polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. Strain W12T has a genome of 7.42 Mb with 49.7 mol% G+C content. Nine copies of 16S rRNA genes with a maximum dissimilarity of 1.02 % and 13 biosynthetic gene clusters mainly coding for peptide products were predicted in the genome. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that strain W12T represents a novel species in the genus Dictyobacter . The most closely related Dictyobacter type strain was Dictyobacter alpinus Uno16T, with 16S rRNA gene sequence similarity and genomic average nucleotide identity of 98.37 % and 80.00 %, respectively. Herein, we propose the name Dictyobacter vulcani sp. nov. for the type strain W12T (=NBRC 113551T=BCRC 81169T) in the bacterial class Ktedonobacteria .

Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria

The prevalence of antibiotic resistance and the decrease in novel antibiotic discovery in recent years necessitates the identification of potentially novel microbial resources to produce natural products. Ktedonobacteria, a class of deeply branched bacterial lineage in the ancient phylum Chloroflexi, are ubiquitous in terrestrial environments and characterized by their large genome size and complex life cycle. These characteristics indicate Ktedonobacteria as a potential active producer of bioactive compounds. In this study, we observed the existence of a putative "megaplasmid," multiple copies of ribosomal RNA operons, and high ratio of hypothetical proteins with unknown functions in the class Ktedonobacteria. Furthermore, a total of 104 antiSMASH-predicted putative biosynthetic gene clusters (BGCs) for secondary metabolites with high novelty and diversity were identified in nine Ktedonobacteria genomes. Our investigation of domain composition and organization of the non-ribosomal peptide synthetase and polyketide synthase BGCs further supports the concept that class Ktedonobacteria may produce compounds structurally different from known natural products. Furthermore, screening of bioactive compounds from representative Ktedonobacteria strains resulted in the identification of broad antimicrobial activities against both Gram-positive and Gram-negative tested bacterial strains. Based on these findings, we propose the ancient, ubiquitous, and spore-forming Ktedonobacteria as a versatile and promising microbial resource for natural product discovery.

Analysis of carbohydrate-active enzymes in Thermogemmatispora sp. strain T81 reveals carbohydrate degradation ability

The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.