scholarly journals Microbial Communities and Sulfate-Reducing Microorganisms Abundance and Diversity in Municipal Anaerobic Sewage Sludge Digesters from a Wastewater Treatment Plant (Marrakech, Morocco)

Processes ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. 1284
Author(s):  
Abdelaziz El Houari ◽  
Magali Ranchou-Peyruse ◽  
Anthony Ranchou-Peyruse ◽  
Rhizlane Bennisse ◽  
Radia Bouterfas ◽  
...  
Keyword(s):  
Treatment Plant ◽  
16S Rrna Gene Sequencing ◽  
Global Scale ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Sulfate Reducing ◽  
Dsrb Gene ◽  
Rrna Gene Sequencing ◽  
Abundance And Diversity ◽  
And Function

Both molecular analyses and culture-dependent isolation were combined to investigate the diversity of sulfate-reducing prokaryotes and explore their role in sulfides production in full-scale anaerobic digesters (Marrakech, Morocco). At global scale, using 16S rRNA gene sequencing, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Synergistetes, and Euryarchaeota were the most dominant phyla. The abundance of Archaea (3.1–5.7%) was linked with temperature. The mcrA gene ranged from 2.18 × 105 to 1.47 × 107 gene copies.g−1 of sludge. The sulfate-reducing prokaryotes, representing 5% of total sequences, involved in sulfides production were Peptococcaceae, Syntrophaceae, Desulfobulbaceae, Desulfovibrionaceae, Syntrophobacteraceae, Desulfurellaceae, and Desulfobacteraceae. Furthermore, dsrB gene ranged from 2.18 × 105 to 1.92 × 107 gene copies.g−1 of sludge. The results revealed that exploration of diversity and function of sulfate-reducing bacteria may play a key role in decreasing sulfide production, an undesirable by-product, during anaerobic digestion.

scholarly journals Spatially-resolved correlative microscopy and microbial identification reveals dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

2020 ◽  
Author(s):  
Jeffrey Marlow ◽  
Rachel Spietz ◽  
Keun-Young Kim ◽  
Mark Ellisman ◽  
Peter Girguis ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Community Members ◽  
Marsh Sediment ◽  
Anabolic Activity ◽  
Salt Marsh Sediment ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractCoastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were embedded and analyzed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ∼60% in the top cm to 10-25% between 2-7 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase, and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.Statement of SignificanceMicroscale spatial relationships dictate critical aspects of a microbiome’s inner workings and emergent properties, such as evolutionary pathways, niche development, and community structure and function. However, many commonly used methods in microbial ecology neglect this parameter – obscuring important microbe-microbe and microbe-mineral interactions – and instead employ bulk-scale methodologies that are incapable of resolving these intricate relationships.This benchmark study presents a compelling new approach for exploring the anabolic activity of a complex microbial community by mapping the precise spatial configuration of anabolically active organisms within mineralogically heterogeneous sediment through in situ incubation, resin embedding, and correlative fluorescence and electron microscopy. In parallel, active organisms were identified through fluorescence-activated cell sorting and 16S rRNA gene sequencing, enabling a powerful interpretive framework connecting location, identity, activity, and putative biogeochemical roles of microbial community members.We deploy this novel approach in salt marsh sediment, revealing quantitative insights into the fundamental principles that govern the structure and function of sediment-hosted microbial communities. In particular, at different sediment horizons, we observed striking changes in the proportion of anabolically active cells, the identities of the most prominent active community members, and the nature of microbe-mineral affiliations. Improved approaches for understanding microscale ecosystems in a new light, such as those presented here, reveal environmental parameters that promote or constrain metabolic activity and clarify the impact that microbial communities have on our world.

scholarly journals Diversity of siderophore-producing bacterial cultures from Carlsbad Caverns National Park caves, Carlsbad, New Mexico

2021 ◽  
Vol 83 (1) ◽  
pp. 29-43
Author(s):  
Tammi Duncan ◽  
Margaret Werner-Washburne ◽  
Diana Northup
Keyword(s):  
National Park ◽  
Ferric Iron ◽  
16S Rrna Gene Sequencing ◽  
Siderophore Production ◽  
Rrna Gene ◽  
Hydroxamate Siderophores ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
Ferromanganese Deposits

Siderophores are microbially-produced ferric iron chelators. They are essential for microbial survival, but their presence and function for cave microorganisms have not been extensively studied. Siderophores are classified based on the common functional groups (catechols, hydroxamates, carboxylates, and mixed) that coordinate to ferric (Fe3+) iron. Cave environments are nutrient-limited and previous evidence suggests siderophore usage in carbonate caves. We hypothesize that siderophores are likely used as a mechanism in caves to obtain critical ferric iron. Cave bacteria were collected from long-term parent cultures (LT PC) or short-term parent cultures (ST PC) inoculated with ferromanganese deposits (FMD) and carbonate secondary minerals from Lechuguilla and Spider caves in Carlsbad Caverns National Park, NM. LT PC were incubated for 10−11 years to identify potential chemolithoheterotrophic cultures able to survive in nutrient-limited conditions. ST PC were incubated for 1−3 days to identify a broader diversity of cave isolates. A total of 170 LT and ST cultures, 18 pure and 152 mixed, were collected and used to classify siderophore production and type and to identify siderophore producers. Siderophore production was slow to develop (>10 days) in LT cultures with a greater number of weak siderophore producers in comparison to the ST cultures that produced siderophores in <10 days, with a majority of strong siderophore producers. Overall, 64% of the total cultures were siderophore producers, with the majority producing hydroxamate siderophores. Siderophore producers were classified into Proteobacteria (Alpha-, Beta-, or Gamma-), Actinobacteria, Bacteroidetes, and Firmicutes phyla using 16S rRNA gene sequencing. Our study supports our hypothesis that cave bacteria have the capability to produce siderophores in the subsurface to obtain critical ferric iron.

scholarly journals Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

2021 ◽  
Author(s):  
Yumiko Okamoto ◽  
Natsumi Ichinohe ◽  
Cheolwoon Woo ◽  
Sung-Yong Han ◽  
Hyeong-Hoo Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Lutra Lutra ◽  
Rrna Gene ◽  
Baseline Information ◽  
The Difference ◽  
Rrna Gene Sequencing ◽  
And Function

AbstractUnderstanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.

scholarly journals Altered Gut Microbiota Associated with Hemorrhage in Chronic Radiation Proctitis

2020 ◽  
Author(s):  
Liangzhe Liu ◽  
Bingcheng Chen ◽  
Chaoyun Chen ◽  
Chen Ding ◽  
Nana Xiao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Radiation Proctitis ◽  
Rrna Gene ◽  
Chronic Radiation Proctitis ◽  
Chronic Radiation ◽  
Pelvic Cancer ◽  
Metagenomic Study ◽  
Rrna Gene Sequencing ◽  
And Function

Abstract Background: Pelvic cancer radiotherapy may cause chronic radiation proctitis (CRP) that adversely affects patient’s quality of life. Here, we aimed to characterize the gut microbiota of CRP patients and reveal the association of dysbiosis and hematochezia. A comparative metagenomic study of CRP with and without hematochezia was conducted by 16S rRNA gene sequencing. Results: Different patterns of dysbiosis were observed in CRP patients with and without hematochezia. The abundance of Bacteroides was higher in CRP patients without hematochezia. The Verrucomicrobia phylum was enriched while the compositions of the Enterobacteriales family and the Porphyromonadaceae genus were relatively lower in the microbiota of CRP patients with hematochezia. PICRUSt analysis suggested that the expression of Fe-S protein, Glutathione peroxidase and Glutaredoxin-related protein were increased, indicating an exacerbated inflammation state in hematochezia patients. Conclusions: This study provides new insight to the altered composition and function of gut microbiota in patients with hematochezia, implying the link of CRP symptom and bacterial ecosystem on rectal epithelial layer.

scholarly journals Gut Microbiota and Metabolome Alterations Associated with Chinese Monks’ Practice

2022 ◽  
Author(s):  
Tingting Qiao ◽  
Ganghua Lu ◽  
Zhongwei Lv ◽  
Dan Li ◽  
Chengyou Jia ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Flora ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
Mental Events ◽  
The Relationship

Abstract BackgroundThe practices of monks mainly include long-term vegetarianism and meditation, which are likely to fundamentally influence the gut microbiota and fecal metabolites. We aim to study the relationship between the practices of Chinese monks and gut microbiotas and metabolites.MethodsTwenty-four monks and forty-eight omnivorous controls (never meditated) were included. The microbiotas of all samples were profiled by 16S rRNA gene sequencing, and the metabolomes were examined by nontargeted LC–MS metabolomics. Twenty-four monks were divided into the H group and the L group according to the median time of practice, and microbiota and metabolite analyses were carried out in the two groups.ResultsMicrobial communities and metabolites were decreased in monks. Bacteroidetes was increased in monks, while the Firmicutes, Actinobacteria, and Firmicutes/Bacteroidetes ratios were decreased. At the genus level, Faecalibacterium, Lachnospira, Roseburia, norank_f__Lachnospiraceae, etc. were higher in monks, while Blautia, Eubacterium__hallii_group, Bifidobacteria, etc. were lower (all p < 0.05). Most identical KEGG categories in both Tax4Fun and PICRUSt2 were related to metabolism (6/8, 75.0%). Most higher abundance genera were positively correlated with higher abundance metabolites in monks, indicating that intestinal flora significantly affects intestinal metabolic function. Lipids and lipid-like molecules were the major differential metabolites (VIP >2, p < 0.05) in the two groups. L-dopa plays an important role in many metabolic pathways in monks. Prevotella_9 was enriched in the L group, while norank_f__Lachnospiraceae was enriched in the H group. DG (16:0/18:0/0:0) was highly expressed in the H group and participated in sixteen KEGG functional pathways as well as many immune-related KEGG enrichment pathways.ConclusionThe monks' lifestyle practices of vegetarianism and meditation have the potential to modulate human metabolism and function by affecting the gut microbial composition and metabolites. The appropriate practice of monks makes the intestine younger and increases immunity, but long-term practice may cause adverse physical and mental events.

scholarly journals Combined Intestinal Metabolomics and Microbiota Analysis for Acute Endometritis Induced by Lipopolysaccharide in Mice

2021 ◽  
Vol 11 ◽  
Author(s):  
Yuqing Dong ◽  
Yuan Yuan ◽  
Yichuan Ma ◽  
Yuanyue Luo ◽  
Wenjing Zhou ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bacterial Infections ◽  
16S Rrna Gene Sequencing ◽  
Control Group ◽  
Rrna Gene ◽  
Chronic Infections ◽  
Intestinal Microbes ◽  
Specific Pathogen ◽  
Rrna Gene Sequencing ◽  
And Function

Endometritis is generally caused by bacterial infections, including both acute and chronic infections. In the past few decades, accumulated evidence showed that the occurrence of diseases might be related to gut microbiota. The progression of diseases is previously known to change the composition and diversity of intestinal microbiota. Additionally, it also causes corresponding changes in metabolites, primarily by affecting the physiological processes of microbiota. However, the effects of acute endometritis on intestinal microbiota and its metabolism remain unknown. Thus, the present study aimed to assess the effects of acute endometritis on intestinal microbes and their metabolites. Briefly, endometritis was induced in 30 specific pathogen-free (SPF) BALB/c female mice via intrauterine administration of lipopolysaccharide (LPS) after anesthesia. Following this, 16S rRNA gene sequencing and liquid chromatogram-mass spectrometry (LC-MS) were performed. At the genus level, the relative abundance of Klebsiella, Lachnoclostridium_5, and Citrobacter was found to be greater in the LPS group than in the control group. Importantly, the control group exhibited a higher ratio of Christensenellaceae_R−7_group and Parasutterella. Furthermore, intestinal metabolomics analysis in mice showed that acute endometritis altered the concentration of intestinal metabolites and affected biological oxidation, energy metabolism, and biosynthesis of primary bile acids. The correlation analysis between microbial diversity and metabolome provided a basis for a comprehensive understanding of the composition and function of the microbial community. Altogether, the findings of this study would be helpful in the prevention and treatment of acute endometritis in the future.

scholarly journals Response of Sediment Bacterial Communities to Sudden Vegetation Dieback in a Coastal Wetland

2017 ◽  
Vol 1 (1) ◽  
pp. 5-13 ◽  
Author(s):  
Wade H. Elmer ◽  
Peter Thiel ◽  
Blaire Steven
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Coastal Wetland ◽  
16S Rrna Gene Sequencing ◽  
Sediment Chemistry ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Initial Appearance ◽  
Rrna Gene Sequencing ◽  
Soil Mix

There is an increasing recognition of the role coastal vegetated ecosystems play in atmospheric carbon sequestration. However, the development of sudden vegetation dieback (SVD), a phenomenon that causes the rapid death of Spartina alterniflora, followed by no or slow recovery, has affected large-scale alterations in Atlantic coastal systems. This study reports the effects of the development of SVD on the sediment microbial communities. In 1999, Hammonasset Beach State Park in Connecticut experienced the initial appearance of SVD. After more than a decade, the plants have not recovered. Yet, sediment chemistry was similar between vegetated and SVD affected sites, with the exception of water loading, which was significantly higher in the SVD affected sites. Soil CO2 flux, a proxy for soil respiration, was reduced by 64% in SVD sites compared with sites that remained vegetated. This suggests that SVD has affected large changes in carbon cycling in the wetland sediments. The microbial communities between vegetated and SVD sites were significantly different, as assessed by 16S rRNA gene sequencing. The vegetated sediments harbored significantly higher populations of Bacteroidetes-related bacteria, whereas the SVD affected sediments contained a significantly enriched relative abundance of sulfate-reducing bacteria, predominantly within the genus Desulfobulbus. Thus, the development of SVD appears to favor anaerobic metabolic pathways at the expense of saprophytes. Greenhouse experiments testing if the alterations in the sediment microbial communities were associated with differences in S. alterniflora germination or growth were also pursued. Although small differences in growth and disease ratings were noted between seedling and transplants grown in soil mix (control), autoclaved SVD sediments, or non-autoclaved (natural) SVD sediments, mortality was not significantly different, indicating that the alterations in the sediment communities are not likely responsible for SVD, or a primary cause for the failure of S. alterniflora to recolonize the SVD sites.

Alterations of gut microbiome in patients with type 2 diabetes mellitus who had undergone cholecystectomy

2021 ◽  
Vol 320 (1) ◽  
pp. E113-E121
Author(s):  
Bin Wei ◽  
Yakun Wang ◽  
Shoukui Xiang ◽  
Yan Jiang ◽  
Rong Chen ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
New Onset

The gut microbiome of long-term T2DM patients who had undergone cholecystectomy and age- and/or sex-matched subjects of new-onset and long-term T2DM without cholecystectomy was assessed using 16S rRNA gene sequencing in stool samples. The findings suggest that, cholecystectomy could partially alleviate long-term diabetes-induced dysbiosis of gut microbiome composition and function.

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