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BMC Genomics Feb 2024Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly...
Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflorum (GD) and Geodorum attenuatum (GA) are widespread species. The growth of orchids depend on microorganisms. However, there are few studies on the microbial structure in Geodorum, and little is known about the roles of microorganisms in the endangered mechanism of G. eulophioides. This study analyzed the structure and composition of bacterial and fungal communities in the roots and rhizosphere soil of GE, GD, and GA. The results showed that Delftia, Bordetella and norank_f_Xanthobacteraceae were the dominant bacteria in the roots of Geodorum, while norank_f_Xanthobacteraceae, Gaiella and norank_f_norank_o_Gaiellales were the dominant bacteria in the rhizosphere soil of Geodorum. In the roots, the proportion of Mycobacterium in GD_roadside was higher than that in GD_understory, on the contrary, the proportion of Fusarium, Delftia and Bordetella in GD_roadside was lower than that in GD_understory. Compared with the GD_understory, the roots of GD_roadside had lower microbial diversity. In the endangered species GE, Russula was the primary fungus in the roots and rhizosphere soil, with fungal diversity lower than in the more widespread species. Among the widespread species, the dominant fungal genera in the roots and rhizosphere soil were Neocosmospora, Fusarium and Coprinopsis. This study enhances our understanding of microbial composition and diversity, providing fundamental information for future research on microbial contributions to plant growth and ecosystem function in Geodorum.
Topics: Rhizosphere; Soil; Ecosystem; Fungi; Soil Microbiology; Agaricales; Plant Roots; Bacteria; Fusarium
PubMed: 38418975
DOI: 10.1186/s12864-024-10143-2 -
Frontiers in Microbiology 2023This study aimed to explore the differences between Eucommiae cortex (EC) endophytic bacteria from different origins and their effects on the active ingredients of EC.
OBJECTIVE
This study aimed to explore the differences between Eucommiae cortex (EC) endophytic bacteria from different origins and their effects on the active ingredients of EC.
METHODS
A total of 10 samples of Oliv. () bark were collected from each of the following four regions, namely, Zunyi in Guizhou (GZ), Baokang in Hubei (HUB), Cili in Hunan (HUN), and Loyang in Shaanxi (SX). Subsequently, the contents of the main active ingredients of EC were determined by ultra-performance liquid chromatography (UPLC), and the endophytic bacteria of EC were detected by 16S rRNA sequencing. The relationship between the dominant endophytic bacteria and the active ingredients was investigated by correlation analysis.
RESULTS
A total of 4,551 different operational taxonomic units (OTUs) were delineated in the four groups of samples, of which 585, 439, 957, and 684 genera were annotated from GZ, HUB, HUN, and SX, respectively. The richness and diversity of endophytic bacteria from different origins were ranked as HUN > SX > GZ or HUB. The analysis demonstrated that there was no significant correlation between the diversity and richness of endophytic bacteria in EC and its active ingredients. Nevertheless, notable variations in the community structures of endophytic bacteria were observed across different origins, and they had a considerable impact on certain active ingredients in EC. and were the dominant genera. Characteristic bacteria of different origins could be clearly distinguished. Simultaneous, significant correlations had been identified between some characteristic endophytic bacteria derived from different origins and active ingredients of EC. For example, , a characteristic bacterium from GZ, showed a significant positive correlation with pinoresinol diglucoside. and , two characteristic bacteria from HUB, exhibited significant positive correlations with geniposidic acid. , a characteristic bacterium from HUN, demonstrated a significant positive correlation with geniposide. , a characteristic bacterium from SX, displayed a significant positive correlation with pinoresinol diglucoside.
CONCLUSION
There was a complex correlation between EC endophytic bacteria and active ingredient content, while EC endophytic bacteria from different origins had significant differences at the genus level.
PubMed: 37266017
DOI: 10.3389/fmicb.2023.1164674 -
Bioresources and Bioprocessing Oct 2023Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process....
Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.
PubMed: 38647588
DOI: 10.1186/s40643-023-00694-9 -
The ISME Journal Nov 2023Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms...
Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.
Topics: Arsenic; Soil; Symbiosis; Ecosystem; Pyruvic Acid; Bacteria; Glucose
PubMed: 37737252
DOI: 10.1038/s41396-023-01519-5 -
Current Microbiology Jan 2023Microbes use both organic and inorganic compounds as electron donors, with different electronic potentials, to produce energy required for growth in environments....
Microbes use both organic and inorganic compounds as electron donors, with different electronic potentials, to produce energy required for growth in environments. Conventional studies on the effects of different electron donors on microbial community has been extensively studied with a set cathode potential. However, it remains under-researched how a microbial community response to the different redox potentials in different environments. Here, we incubated a lake sediment in a single-chamber reactor equipped with three working electrodes, i.e., with potentials of - 0.29 V, - 0.05 V versus standard hydrogen electrode and open-circuit, respectively. Results reveal that the structure of bacterial communities was highly similar for all closed-circuit electrodes (- 0.29 V, - 0.05 V), while differing significantly from those on open-circuit electrodes. We also show that specific bacteria were preferentially enriched by different electrode potentials, i.e., Pseudomonas and Rhodobacter preferentially grew on - 0.05 V and - 0.29 V cathode potentials, Azospirillum and Bosea preferentially grew on - 0.05 V; while Ferrovibrio, Hydrogenophaga, Delftia, and Sphingobium preferentially grew on - 0.29 V. In addition, microorganisms selectively enriched on open-circuit electrodes possess higher connectivity and closer relationship than microorganisms selectively enriched on closed-circuit electrode.
Topics: Bioelectric Energy Sources; Bacteria; Microbiota; Electrodes
PubMed: 36609874
DOI: 10.1007/s00284-022-03148-1 -
Animals : An Open Access Journal From... Dec 2023The present study was carried out to determine the seminal microbiota of boars and their correlation with sperm quality. A total of 17 ejaculates were collected from 17...
The present study was carried out to determine the seminal microbiota of boars and their correlation with sperm quality. A total of 17 ejaculates were collected from 17 Duroc boars and were classified according to sperm quality into two groups: low-quality ( = 8) and high-quality ( = 9). Each ejaculate was subjected to (i) semen evaluation, (ii) bacterial culture and MALDI-TOF identification, and (iii) 16S rRNA gene sequencing and bioinformatic analyses. No difference in the total bacterial count, alpha diversity, and beta diversity between the high-quality group and the low-quality group was detected ( > 0.05). While was negatively correlated with sperm quality ( < 0.05), was positively correlated with sperm quality ( < 0.05). Lactobacillales (25.2%; LB) and Enterobacterales (10.3%; EB) were the most dominant bacteria and negatively correlated: EB = 507.3 - 0.5 × LB, R = 0.24, < 0.001. Moreover, the abundance of was negatively correlated with LB (r = -0.754, < 0.001) and positively correlated with (r = 0.533, < 0.05). was positively correlated with (r = 0.485, < 0.05), (r = 0.622, < 0.01), and (r = 0.489, < 0.05). In conclusion, seminal microbiota is significantly associated with boar semen qualities. The distributions of the most dominant bacterial genera, the differences in the abundance of small subset microbes, and their correlation appear to have far more impact than the overall seminal bacterial content (e.g., total bacterial count, alpha diversity, and beta diversity) on sperm quality.
PubMed: 38136874
DOI: 10.3390/ani13243837 -
Polish Journal of Microbiology Sep 2020Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the...
Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera , and that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium ( < 0.05), but not in sterilized STE influent water ( > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater. Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera , and that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium ( < 0.05), but not in sterilized STE influent water ( > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater.
Topics: Aerobiosis; Bacteria; Biodegradation, Environmental; Delftia; Denitrification; Heterotrophic Processes; Microbiota; Nitrification; Sewage; Waste Disposal, Fluid
PubMed: 32189483
DOI: 10.33073/pjm-2020-013 -
Environmental Monitoring and Assessment Mar 2022The alarming upsurge in the co-existence of heavy metal and antibiotic resistance may have a devastating impact on humans, animals, and the environment. Four...
The alarming upsurge in the co-existence of heavy metal and antibiotic resistance may have a devastating impact on humans, animals, and the environment. Four metal-resistant bacteria were isolated from hospital effluents and industrial drain. Heavy metal resistance and antimicrobial resistance were examined in the isolates followed by identification through 16S rRNA gene sequencing. Delftia tsuruhatensis strain FK-01 and Carnobacterium inhibens strain FK-02 tolerated arsenic with maximal tolerated concentration (MTC) of 30 mM and 10 mM, respectively. Staphylococcus hominis strain FK-04 tolerated copper up to 4 mM and lead-resistant Raoultella ornithinolytica strain FK-05 exhibited tolerance to 1 mM lead. The growth kinetics of bacteria were monitored in the presence of metals and the following antibiotics, tetracycline, chloramphenicol, and kanamycin. The presence of arsenate significantly enhanced tetracycline resistance in C. inhibens. Heavy metal-induced antibiotic resistance was also observed in S. hominis and R. ornithinolytica, against chloramphenicol and tetracycline respectively. D. tsuruhatensis showed resistance to kanamycin but when grown in the presence of arsenic and kanamycin, bacteria lost resistance to the antibiotic. Therefore, it is suggested that the novel arsenate-resistant strain Delftia tsuruhatensis FK-01 has a unique ability to inhibit antimicrobial resistance that can be harnessed in bioremediation.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Bacterial; Environmental Monitoring; Humans; Metals, Heavy; RNA, Ribosomal, 16S; Wastewater
PubMed: 35254524
DOI: 10.1007/s10661-022-09917-6 -
Nutrients Oct 2022Preclinical studies have demonstrated that intrauterine growth retardation (IUGR) is associated with reduced lung development during the neonatal period and infancy....
Preclinical studies have demonstrated that intrauterine growth retardation (IUGR) is associated with reduced lung development during the neonatal period and infancy. Uteroplacental insufficiency (UPI), affecting approximately 10% of human pregnancies, is the most common cause of IUGR. This study investigated the effects of UPI on lung development and the intestinal microbiota and correlations in newborn rats with IUGR, using bilateral uterine artery ligation to induce UPI. Maternal fecal samples were collected on postnatal day 0. On postnatal days 0 and 7, lung and intestinal microbiota samples were collected from the left lung and the lower gastrointestinal tract. The right lung was harvested for histological assessment and Western blot analysis. Results showed that UPI through bilateral uterine artery ligation did not alter the maternal gut microbiota. IUGR impaired lung development and angiogenesis in newborn rats. Moreover, on postnatal day 0, the presence of and in the lungs and and in the gastrointestinal tract was negatively correlated with lung development. in the lungs and and in the gastrointestinal tract were negatively correlated with lung development on day 7. UPI may have regulated lung development and angiogenesis through the modulation of the newborn rats' intestinal and lung microbiota.
Topics: Pregnancy; Female; Humans; Animals; Rats; Placental Insufficiency; Animals, Newborn; Rats, Sprague-Dawley; Fetal Growth Retardation; Lung; Microbiota
PubMed: 36297072
DOI: 10.3390/nu14204388 -
PloS One 2022This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different...
This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different degradation periods was analyzed using MiSeq high-throughput sequencing. The results showed that 14 days after inoculation, the filter paper enzyme and endoglucanase activities increased to 2.55 U·mL-1 and 2.34 U·mL-1. The xylanase, laccase, and lignin peroxidase activities rose to 9.86 U·mL-1, 132.16 U·L-1, and 85.43 U·L-1 after 28 d, which was consistent with changes in the straw degradation rate. The degradation rates of straw, lignin, cellulose, and hemicellulose were 31.43%, 13.67%, 25.04%, and 21.69%, respectively, after 28 d of fermentation at 15°C. Proteobacteria, Firmicutes, and Bacteroidetes were the main bacterial species in samples at different degradation stages. The dominant genera included Pseudomonas, Delftia, and Paenibacillus during the initial stage (1 d, 7 d) and the mid-term stage (14 d). The key functional microbes during the late stage (21 d, 28 d) were Rhizobium, Chryseobacterium, Sphingobacterium, Brevundimonas, and Devosia. Changes in the bacterial consortium structure and straw degradation characteristics during different degradation periods were clarified to provide a theoretical basis for the rational utilization of microbial decomposer M44.
Topics: Bacteria; Cellulose; Fermentation; Lignin; Microbial Consortia; Temperature
PubMed: 35802565
DOI: 10.1371/journal.pone.0270162