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Applied and Environmental Microbiology Jun 2024Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial...
Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. , Comamonadaceae, and were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.
PubMed: 38940583
DOI: 10.1128/aem.00714-24 -
Archives of Microbiology Jun 2024Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are...
Ten strains of psychrotolerant methylotrophic bacteria were isolated from the samples collected in Larsemann and Bunger Hills (Antarctica). Most of the isolates are assigned to the genus Pseudomonas, representatives of the genera Janthinobacterium, Massilia, Methylotenera and Flavobacterium were also found. Majority of isolates were able to grow on a wide range of sugars, methylamines and other substrates. Optimal growth temperatures for the isolated strains varied from 6 °C to 28 °C. The optimal concentration of NaCl was 0.5-2.0%. The optimal pH values of the medium were 6-7. It was found that three strains synthesized indole-3-acetic acid on a medium with L-tryptophan reaching 11-12 μg/ml. The values of intracellular carbohydrates in several strains exceeded 50 μg/ml. Presence of calcium-dependent and lanthanum-dependent methanol dehydrogenase have been shown for some isolates. Strains xBan7, xBan20, xBan37, xBan49, xPrg27, xPrg48, xPrg51 showed the presence of free amino acids. Bioprospection of Earth cryosphere for such microorganisms has a potential in biotechnology.
Topics: Antarctic Regions; Biotechnology; Phylogeny; Indoleacetic Acids; Methylobacteriaceae; Hydrogen-Ion Concentration; RNA, Ribosomal, 16S; Cold Temperature; Sodium Chloride; Culture Media; Tryptophan
PubMed: 38907777
DOI: 10.1007/s00203-024-04056-7 -
Cureus May 2024genus was initially described in 1993 as a "pink coccoid." It is a non-fermentative, aerobic, and gram-negative bacteria. This genus has been uncovered in diverse...
genus was initially described in 1993 as a "pink coccoid." It is a non-fermentative, aerobic, and gram-negative bacteria. This genus has been uncovered in diverse environmental niches, ranging from water and soil to air and plants. Despite its prevalence in the natural world, human infections stemming from species remain a rare occurrence. This organism is also known to be resistant to standard antibiotics. We present a case of an 85-year-old woman with (RG) bacteremia who is a resident at an assisted living facility. Healthcare providers should consider this bacterium in slow-developing gram-negative infections, potentially opting for broad-spectrum antibiotics as an initial treatment.
PubMed: 38899252
DOI: 10.7759/cureus.60667 -
Antonie Van Leeuwenhoek Jun 2024Two novel Gram-stain-negative strains designated P7 and P8, were isolated from the soil of a paddy field in Goyang, Republic of Korea, and identified as new species...
Two novel Gram-stain-negative strains designated P7 and P8, were isolated from the soil of a paddy field in Goyang, Republic of Korea, and identified as new species within the genus Roseateles through a polyphasic taxonomic approach. These aerobic, rod-shaped, non-sporulating strains demonstrated optimal growth at 30 °C, pH 7, and in the absence of NaCl (0% w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated close relationships with Roseateles saccharophilus DSM654 (98.7%) and Roseateles puraquae CCUG 52769 (98.96%), respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates with the most closely related strains with publicly available whole genomes were 82.0-85.5% and 25.0-30.2%, respectively. The predominant fatty acids identified were C and summed feature 3 (composed of C ω6c and/or C ω7c), with minor amounts of C, C 3-OH and summed feature 8 (composed of C ω7c and/or C ω6c; 26.4%). Ubiquinone 8 was the main quinone, and the polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, two unidentified phosphoaminolipids, one unidentified phosphoglycolipid, three unidentified phospholipids, and one unidentified aminolipid. The draft genome sequences revealed genomic DNA G + C contents of 70.1% for P7 and 68.2% for P8. Comprehensive physiological, biochemical, and 16S rRNA sequence analyses confirm these isolates as novel species of the genus Roseateles, proposed to be named Roseateles caseinilyticus sp. nov for strain P7 (= KACC 22504 = TBRC 15694) and Roseateles cellulosilyticus sp. nov. for strain P8 (= KACC 22505 = TBRC 15695).
Topics: Soil Microbiology; Phylogeny; RNA, Ribosomal, 16S; Oryza; DNA, Bacterial; Fatty Acids; Base Composition; Republic of Korea; Bacterial Typing Techniques; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Sequence Analysis, DNA
PubMed: 38833203
DOI: 10.1007/s10482-024-01988-4 -
Antonie Van Leeuwenhoek May 2024An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021, was isolated from a black soil sample in Harbin, Heilongjiang province, China....
An aerobic, Gram-stain-negative, motile rod bacterium, designated as SYSU BS000021, was isolated from a black soil sample in Harbin, Heilongjiang province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Methylobacterium, and showed the highest sequence similarity to Methylobacterium segetis KCTC 62267 (98.51%) and Methylobacterium oxalidis DSM 24028 (97.79%). Growth occurred at 20-37℃ (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0% (w/v) NaCl. Polar lipids comprised of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified polar lipid. The major cellular fatty acids (> 5%) were C and C ω7c and/or C ω6c. The predominant respiratory quinone was Q-10. The genomic G + C content was 68.36% based on the whole genome analysis. The average nucleotide identity (≤ 83.5%) and digital DNA-DNA hybridization (≤ 27.3%) values between strain SYSU BS000021 and other members of the genus Methylobacterium were all lower than the threshold values recommended for distinguishing novel prokaryotic species. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain SYSU BS000021 represents a novel species of the genus Methylobacterium, for which the name Methylobacterium nigriterrae sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000021 (= GDMCC 1.3814 = KCTC 8051).
Topics: Soil Microbiology; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Base Composition; Fatty Acids; Methylobacterium; Bacterial Typing Techniques; China; Nucleic Acid Hybridization; Sequence Analysis, DNA; Phospholipids
PubMed: 38806744
DOI: 10.1007/s10482-024-01981-x -
International Journal of Systematic and... May 2024Two strictly aerobic and rod-shaped bacteria, labelled as DB1703 and DB2414S, were obtained from an automobile air conditioning system. Strain DB1703 was...
Two strictly aerobic and rod-shaped bacteria, labelled as DB1703 and DB2414S, were obtained from an automobile air conditioning system. Strain DB1703 was Gram-stain-negative, while strain DB2414S was Gram-stain-positive. Both strains were catalase-positive and oxidase-negative. Strains DB1703 and DB2414S were able to grow at 18-42 °C. Strain DB1703 grew within a NaCl range of 0-3 % and a pH range of 6.0-8.0; while strain DB2414S grew at 0-1 % and pH 6.5-8.5. The phylogenetic and 16S rRNA gene sequence analysis indicated that strains DB1703 and DB2414S belonged to the genera and , respectively. Strain DB1703 showed the closest phylogenetic similarity to YIM 100770 (94.8 %), whereas strain DB2414S was most closely related to ATCC BAA-1496 (97.7 %). The genome sizes of strains DB1703 and DB2414S were 4 652 148 and 4 282 418 bp, respectively, with DNA G+C contents of 68.8 and 70.5 mol%, respectively. Chemotaxonomic data showed Q-10 as the sole ubiquinone in DB1703 and ML-8 (H4) in DB2414S. The predominant cellular fatty acid in DB1703 was summed feature 8 (C 7 and/or C 6), whereas iso-C, C 8, and iso-C were dominant in DB2414S. Overall, the polyphasic taxonomic comparisons showed that strains DB1703 and DB2414S were distinct from their closest taxa and represent novel species within the genera and , respectively. Accordingly, we propose the names sp. nov., with the type strain DB1703 (=KCTC 72724=NBRC 114759), and sp. nov., with the type strain DB2414S (=KCTC 49355=NBRC 114620).
Topics: Phylogeny; Base Composition; Fatty Acids; RNA, Ribosomal, 16S; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Air Conditioning; Ubiquinone; Automobiles; Republic of Korea
PubMed: 38743058
DOI: 10.1099/ijsem.0.006383 -
Animals : An Open Access Journal From... Apr 2024The gut microbiome significantly influences the health and productivity of silkworms (), the cornerstone of sericulture. With the increasing use of cost-effective...
The gut microbiome significantly influences the health and productivity of silkworms (), the cornerstone of sericulture. With the increasing use of cost-effective artificial diets in sericulture, it is crucial to understand how these diets impact the silkworm gut microbiomes. Here we employed 16S rRNA sequencing to delineate the impact of three distinct dietary regimens on the silkworm gut microbiomes: exclusive mulberry leaf diet (SY), exclusive artificial feed diet (SL), and a sequential transition from artificial feed to mulberry leaves (ZS). Our results unveiled stark differences in microbial diversity across the groups, with the ZS group displaying an intermediary complexity. LefSe and random forest analyses identified Methylobacteriaceae, , and as significantly enriched in the ZS group, suggesting their potential to facilitate silkworms' adaptation to dietary transitions. Functional profiling revealed differential pathway regulation, indicating a metabolic reconfiguration in response to dietary modulations. Notably, the enrichment of and in both the SL and ZS groups highlights their potential as probiotics in artificial diets. Our findings provide insights into the diet adaptation mechanisms of silkworm gut microbiota, paving the way for harnessing the intestinal bacteria to enhance silkworm health and silk production through targeted microbial interventions in sericulture practices.
PubMed: 38731265
DOI: 10.3390/ani14091261 -
Journal of Advanced Veterinary and... Mar 2024The objectives of this study were to determine the richness, abundance, and diversity of bacteria in stray dogs () infested by ticks in Comarca Lagunera, northern...
OBJECTIVE
The objectives of this study were to determine the richness, abundance, and diversity of bacteria in stray dogs () infested by ticks in Comarca Lagunera, northern Mexico, and to establish their pathogenic and or/zoonotic potential.
MATERIALS AND METHODS
Blood samples from 12 dogs were collected, and their deoxyribonucleic acid was extracted. The V3-V4 region of the 16S ribosomal ribunocleic acid gene was amplified by polymerase chain reaction. Next-generation sequencing (NGS) was performed on a MiSeq Illumina platform, and the data were analyzed using quantitative insights into microbial ecology.
RESULTS
The operational taxonomic units resulted in 23 phyla, 54 classes, 89 orders, 189 families, 586 genera, and 620 bacterial species; among them, 64 species and/or bacterial genera with pathogenic or zoonotic potential were identified, some of which have been reported in the literature as relevant to public health ( spp spp spp spp spp spp spp and ).
CONCLUSION
This research offers relevant information on the prevalence of tick-borne diseases as well as other potential zoonotic diseases in the blood of stray dogs parasitized by ticks in northern Mexico. New molecular biology and massive NGS techniques may play an important role in the study and documentation of bacterial profiles from animals in close proximity to humans.
PubMed: 38680790
DOI: 10.5455/javar.2024.k757 -
Journal of Hazardous Materials Jun 2024Microcystis typically forms colonies under natural conditions, which contributes to occurrence and prevalence of algal blooms. The colonies consist of Microcystis and...
Dissolved organic matter, calcium ion and extracellular polymeric substances on living associated bacteria of Microcystis colony are crucial for unicellular Microcystis to efficiently form colonies.
Microcystis typically forms colonies under natural conditions, which contributes to occurrence and prevalence of algal blooms. The colonies consist of Microcystis and associated bacteria (AB), embedded in extracellular polymeric substances (EPS). Previous studies indicate that AB can induce Microcystis to form colonies, however the efficiency is generally low and results in a uniform morphotype. In this study, by using filtrated natural water, several AB strains induced unicellular M. aeruginosa to form colonies resembling several Microcystis morphotypes. The mechanisms were investigated with Methylobacterium sp. Z5. Ca was necessary for Z5 to induce Microcystis to form colonies, while dissolved organic matters (DOM) facilitated AB to agglomerate Microcystis to form large colonies. EPS of living Z5, mainly the aromatic protein components, played a key role in colony induction. Z5 initially aggregated Microcystis via the bridging effects of Ca and DOM, followed by the induction of EPS synthesis and secretion in Microcystis. In this process, the colony forming mode shifted from cell adhesion to a combination of cell adhesion and cell division. Intriguingly, Z5 drove the genomic rearrangement of Microcystis by upregulating some transposase genes. This study unveiled a novel mechanism about Microcystis colony formation and identified a new driver of Microcystis genomic evolution.
Topics: Microcystis; Calcium; Extracellular Polymeric Substance Matrix; Methylobacterium
PubMed: 38677120
DOI: 10.1016/j.jhazmat.2024.134352 -
Communications Medicine Apr 2024Atopic dermatitis (AD) is a chronic, inflammatory disease characterized by dry, pruritic skin. In the U.S., the prevalence of AD has increased over three-fold since the...
BACKGROUND
Atopic dermatitis (AD) is a chronic, inflammatory disease characterized by dry, pruritic skin. In the U.S., the prevalence of AD has increased over three-fold since the 1970s. We previously reported a geographic association between isocyanate-containing air pollution and AD as well as mechanistic data demonstrating that isocyanates induce skin dysbiosis and activate the host itch receptor TRPA1. However, non-spatial models are susceptible to spatial confounding and may overlook other meaningful associations.
METHODS
We added spatial analysis to our prior model, contrasting pollution data with clinical visits. In addition, we conducted a retrospective case-control survey of childhood exposure to BTEX-related products. Finally, we assessed implicated compounds, in pure form and as part of synthetic fabric, for their effect on the growth and metabolism of skin commensal bacteria.
RESULTS
Spatial analysis implicate benzene, toluene, ethylbenzene, and, most significantly, xylene (BTEX) compounds. Survey odds ratios for AD were significant for xylene-derived polyester bed sheets (OR = 9.5; CI 2.2-40.1) and diisocyanate-containing wallpaper adhesive (OR = 6.5; CI 1.5-27.8). Staphylococcus aureus lives longer on synthetic textiles compared to natural textiles. Meanwhile, synthetic fabric exposure shifts the lipid metabolism of health-associated commensals (Roseomonas mucosa and S. epidermidis) away from therapeutic pathways.
CONCLUSIONS
We propose that BTEX chemicals in their raw forms and in synthetic products represent a unifying hypothesis for environmentally induced AD flares through their ability to create dysbiosis in the skin microbiota and directly activate TRPA1. Unequal distribution of these pollutants may also influence racial disparities in AD rates.
PubMed: 38637696
DOI: 10.1038/s43856-024-00500-3