dDespite their importance as a biofuel production platform, only a very limited number of butanol-tolerant bacteria have been identified thus far. Here, we extensively explored butanol-and isobutanol-tolerant bacteria from various environmental samples. A total of 16 aerobic and anaerobic bacteria that could tolerate greater than 2.0% (vol/vol) butanol and isobutanol were isolated. A 16S rRNA gene sequencing analysis revealed that the isolates were phylogenetically distributed over at least nine genera: Bacillus, Lysinibacillus, Rummeliibacillus, Brevibacillus, Coprothermobacter, Caloribacterium, Enterococcus, Hydrogenoanaerobacterium, and Cellulosimicrobium, within the phyla Firmicutes and Actinobacteria. Ten of the isolates were phylogenetically distinct from previously identified butanol-tolerant bacteria. Two relatively highly butanol-tolerant strains CM4A (aerobe) and GK12 (obligate anaerobe) were characterized further. Both strains changed their membrane fatty acid composition in response to butanol exposure, i.e., CM4A and GK12 exhibited increased saturated and cyclopropane fatty acids (CFAs) and longchain fatty acids, respectively, which may serve to maintain membrane fluidity. The gene (cfa) encoding CFA synthase was cloned from strain CM4A and expressed in Escherichia coli. The recombinant E. coli showed relatively higher butanol and isobutanol tolerance than E. coli without the cfa gene, suggesting that cfa can confer solvent tolerance. The exposure of strain GK12 to butanol by consecutive passages even enhanced the growth rate, indicating that yet-unknown mechanisms may also contribute to solvent tolerance. Taken together, the results demonstrate that a wide variety of butanol-and isobutanol-tolerant bacteria that can grow in 2.0% butanol exist in the environment and have various strategies to maintain structural integrity against detrimental solvents.
Phylogenetic analysis of bacteria preserved within an ice wedge from the Fox permafrost tunnel was undertaken by cultivation and molecular techniques. The radiocarbon age of the ice wedge was determined. Our results suggest that the bacteria in the ice wedge adapted to the frozen conditions have survived for 25,000 years.
A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov.
Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, JapanA moderately thermophilic, methanol-oxidizing bacterium (strain Gela4 T ) was isolated from methane-utilizing mixed-culture originating from marine sediment near a hydrothermal vent. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain Gela4 T was closely related to members of the genus 'Methyloligella' (94.7 % similarity) within the class Alphaproteobacteria. Strain Gela4 T was a Gram-staining-negative and aerobic organism. Cells were rod-shaped and non-motile. The temperature range for growth of strain Gela4
The Minami-Kanto gas field, where gases are dissolved in formation water, is a potential analogue for a marine gas hydrate area because both areas are characterized by the accumulation of microbial methane in marine turbidite sand layers interbedded with mud layers. This study examined the physicochemical impacts associated with natural gas production and well drilling on the methanogenic activity and composition in this gas field. Twenty-four gas-associated formation water samples were collected from confined sand aquifers through production wells. The stable isotopic compositions of methane in the gases indicated their origin to be biogenic via the carbonate reduction pathway. Consistent with this classification, methanogenic activity measurements using radiotracers, culturing experiments and molecular analysis of formation water samples indicated the predominance of hydrogenotrophic methanogenesis. The cultivation of water samples amended only with methanogenic substrates resulted in significant increases in microbial cells along with high-yield methane production, indicating the restricted availability of substrates in the aquifers. Hydrogenotrophic methanogenic activity increased with increasing natural gas production from the corresponding wells, suggesting that the flux of substrates from organic-rich mudstones to adjacent sand aquifers is enhanced by the decrease in fluid pressure in sand layers associated with natural gas/water production. The transient predominance of methylotrophic methanogens, observed for a few years after well drilling, also suggested the stimulation of the methanogens by the exposure of unutilized organic matter through well drilling. These results provide an insight into the physicochemical impacts on the methanogenic activity in biogenic gas deposits including marine gas hydrates.
Little is known about the microbial distribution patterns in subseafloor sediments. This study examines microbial diversity and activities in sediments of the Nankai Trough, where biogenic gas hydrates are deposited. Illumina sequencing of 16S rRNA genes revealed that the prokaryotic community structure is correlated with hydrate occurrence and depth but not with the sedimentary facies. The bacterial phyla 'Atribacteria' lineage JS1 and Chloroflexi dominated in all samples, whereas lower taxonomic units of Chloroflexi accounted for community variation related to hydrate saturation. In archaeal communities, 'Bathyarchaeota' was significantly abundant in the hydrate-containing samples, whereas Marine Benthic Group-B dominated in the upper sediments without hydrates. mcrA gene sequences assigned to deeply branching groups and ANME-1 were detected only in hydrate-containing samples. A predominance of hydrogenotrophic methanogens, Methanomicrobiales and Methanobacteriales, over acetoclastic methanogens was found throughout the depth. Incubation tests on hydrate-containing samples with a stable isotope tracer showed anaerobic methane oxidation activities under both low- and seawater-like salinity conditions. These results indicate that the distribution patterns of microorganisms involved in carbon cycling changed with gas hydrate occurrence, possibly because of the previous hydrate dissociation followed by pore water salinity decrease in situ, as previously proposed by a geochemical study at the study site.
Functional variation of Rpf, a growth factor found exclusively in Actinobacteria, is differentiated by its source and amino acid sequences. Only purified Rpf proteins from three species have been studied so far. To seek new Rpfs for use in future studies to understand their role in Actinobacteria, the objective of this study was to identify rpf gene homologs in Tomitella biformata AHU 1821T, a novel Actinobacteria isolated from permafrost ice wedge. Amplification using degenerate primers targeting the essential Rpf domain led to the discovery of a new rpf gene in T. biformata. Gene structure and the deduced Rpf domain amino acid sequence indicated that this rpf gene was not identical to previously studied Rpf. Phylogenetic analysis placed T. biformata Rpf in a monophyletic branch in the RpfB subfamily. The deduced amino acid sequence was 44.9% identical to RpfB in Mycobacterium tuberculosis, the closest functionally tested Rpf. The gene was cloned and expressed in Escherichia coli; the recombinant Rpf protein (rRpf) promoted the growth of dividing cells and resuscitated non-dividing cells of T. biformata. Compared to other studies, this Rpf was required at higher concentrations to promote its growth and to resuscitate itself from a non-dividing state. The resuscitation function was likely due to the highly conserved Rpf domain. This study provides evidence that a genetically unique but functional Rpf can be found in novel members of Actinobacteria and can lead to a better understanding of bacterial cytokines in this phylum.
Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge Hokkaido Study Center, University of the Air, N17 W8 Kita-ku, Hokkaido 060-0817, JapanGram-positive, aerobic, non-spore-forming, irregular rod-shaped bacteria, designated strains AHU1791 T and AHU1810, were isolated from a permafrost ice wedge in Alaska. Cells were motile by means of a polar flagellum. The strains were psychrophilic, growing at "5 to 25 6C. Phylogenetic analysis of 16S rRNA gene sequences indicated that the ice-wedge isolates formed a clade distinct from other genera affiliated with the family Microbacteriaceae. The novel strains showed highest levels of 16S rRNA gene sequence similarity with members of the genera Agreia and Subtercola (95.6-95.9 %). The level of 16S rRNA gene sequence similarity between strains AHU1791 T and AHU1810 was 99.8 %. The cell-wall peptidoglycan type of the two strains was B2c, containing 2,4-diaminobutyric acid as the diagnostic amino acid. The predominant menaquinones were MK-12 and MK-13 (strain AHU1791 T ) and MK-11 and MK-12 (strain AHU1810). The major fatty acids of the two strains were 12-methyl tetradecanoic acid (anteiso-C 15 : 0 ), 14-methyl hexadecanoic acid (anteiso-C 17 : 0 ), 14-methyl pentadecanoic acid (iso-C 16 : 0 ) and 13-methyl tetradecanoic acid (iso-C 15 : 0 ). The DNA G+C contents of strains AHU1791 T and AHU1810 were approximately 65 mol%. These phenotypic characteristics differentiated the ice-wedge strains from their closest phylogenetic neighbours, namely Subtercola boreus and the two recognized species of the genus Agreia. The sequences of the housekeeping genes coding for DNA gyrase subunit B (gyrB), RNA polymerase subunit B (rpoB) and recombinase A (recA) were almost identical between strains AHU1791 T and AHU1810.Although the predominant menaquinones found in strains AHU1791 T and AHU1810 were different, no other distinct differences were found with regard to other phenotypic and genotypic characteristics, indicating that the two strains were members of the same species. Accordingly, strains AHU1791 T and AHU1810 are considered to represent a single novel species of a new genus, for which the name Glaciibacter superstes gen. nov., sp. nov. is proposed. The type strain of Glaciibacter superstes is AHU1791 T (5DSM 21135 T 5NBRC 104264 T ).At the time of writing, the family Microbacteriaceae comprises 25 genera that possess a B-type cross-linked peptidoglycan and fully unsaturated respiratory menaquinones. Psychrophilic bacteria within the family, for example members of the genera Cryobacterium (Suzuki et al., 1997; Zhang et al., 2007), Rhodoglobus (Sheridan et al., 2003) and Subtercola (Männistö et al., 2000), have been isolated from cold environments including soils and lakes in Antarctica, glacier ice and groundwater. Previously, weThe GenBank/EMBL/DDBJ accession numbers of the 16S rRNA, gyrB, rpoB and recA gene sequences of strains AHU1791 T and AHU1810 are AB378301 and AB378302 (16S rRNA), AB436916 and AB43691...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.