Coastal Hypoxia Drives Microbial Diversity: Elucidation through 16S rRNA Amplicon Sequencing

Abstract The formation of oxygen-depleted zones in the bottom waters is one of the most widespread phenomena in coastal areas. Upwelling episodes occurring along the west coast of India due to the southwest monsoon lead to an increase in biological productivity which further lowers the dissolved oxygen in the upwelled waters, which intensifies annually between June and October. Here, we have determined the changes in the microbial community in response to the varying oxygen levels and other physicochemical parameters at the Candolim Time Series Station using high-throughput sequencing. Amplicon Sequence Variants across all the samples collected in different seasons were mostly affiliated to the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Firmicutes and Planctomycetes, with the most dominant being Proteobacteria (21-41%). Statistical analysis revealed that microbial diversity differed significantly with changing DO, ammonia, nitrate and nitrite concentrations during different seasons. The microbial community shift due to seasonal hypoxia results in the differential biogeochemical cycling of essential nutrients with certain years seeing redox conditions up to sulphate reduction, while certain years seeing only nitrogen loss. Future scenario of global warming will serve as a big challenge for understanding the role of microbial diversity and its implications in the cycling of natural elements.

Download Full-text

Comparative Analysis of Chicken Cecal Microbial Diversity and Taxonomic Composition in Response to Dietary Variation using 16S rRNA Amplicon Sequencing

10.21203/rs.3.rs-201124/v1 ◽

2021 ◽

Author(s):

Zubia Rashid ◽

Muhammad Zubair Yousaf ◽

Syed Muddassar Hussain Gilani ◽

Sitwat Zehra ◽

Ashaq Ali ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Organic Acids ◽

Microbial Diversity ◽

Relative Abundance ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Feed Additives ◽

Poultry Feed ◽

16S Rrna Amplicon Sequencing

Abstract Antibiotic resistance poses a serious threat to human and animal health. As a consequence, their use in conventional poultry feed may be replaced by non-antibiotic additives (alternatives to antibiotics, ATAs). Phytogenic feed additives and organic acids have been gaining considerable attention that could abate the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. The aim of this study was to evaluate the effects of phytogenic feed additives and organic acids on cecal microbial diversity using 16S rRNA amplicon sequencing of the V3-V4 region. In this study, 240 chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG) and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with an increased microbial diversity in AB, ORG and COM (p < 0.05). The synergistic effects of PHY and ORG increased the population of beneficial bacteria that belonged to the phyla: Firmicutes, Bacteroides and Proteobacteria in the cecum. The presence of the species Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups. In conclusion, treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens.

Download Full-text

Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11475-9 ◽

2021 ◽

Author(s):

Tamara J. H. M. van Bergen ◽

Ana B. Rios-Miguel ◽

Tom M. Nolte ◽

Ad M. J. Ragas ◽

Rosalie van Zelm ◽

...

Keyword(s):

Microbial Community ◽

Activated Sludge ◽

Community Composition ◽

Rate Constants ◽

Wastewater Treatment Plants ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Initial Concentration ◽

Different Seasons

Abstract Pharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs). Biotransformation plays an important role in mitigating environmental risks; however, a mechanistic understanding of involved processes is limited. The aim of this study was to evaluate potential relationships between first-order biotransformation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from WWTP Groesbeek (The Netherlands) of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC–MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing, and kb values were calculated. The biodegradable pharmaceuticals were acetaminophen, metformin, metoprolol, terbutaline, and phenazone (ranked from high to low biotransformation rates). Carbamazepine, diatrizoic acid, diclofenac, and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum, different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetic theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP. Key points • Biotransformation and sorption of pharmaceuticals were assessed in activated sludge. • Higher initial concentrations resulted in higher biotransformation rate constants for biodegradable pharmaceuticals. • Summer and winter inocula produced slightly different biotransformation rate constants although microbial community composition did not significantly change. Graphical abstract

Download Full-text

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

10.1101/114512 ◽

2017 ◽

Cited By ~ 4

Author(s):

Jon G Sanders ◽

Piotr Lukasik ◽

Megan E Frederickson ◽

Jacob A Russell ◽

Ryuichi Koga ◽

...

Keyword(s):

16S Rrna ◽

Microbial Diversity ◽

Tropical Rainforest ◽

Amplicon Sequencing ◽

Sequencing Data ◽

Lowland Tropical Forest ◽

16S Rrna Amplicon Sequencing ◽

Microbial Symbionts ◽

Microbial Symbiosis ◽

Diversity Profiles

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

Download Full-text

Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

10.1101/2020.07.17.209346 ◽

2020 ◽

Author(s):

Kimothy L Smith ◽

Howard A Shuman ◽

Douglas Findeisen

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Water Samples ◽

Ad Hoc ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

The Other ◽

Water Usage ◽

16S Rrna Amplicon Sequencing ◽

Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

Download Full-text

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Microorganisms ◽

10.3390/microorganisms7100416 ◽

2019 ◽

Vol 7 (10) ◽

pp. 416 ◽

Cited By ~ 2

Author(s):

Dyda ◽

Pyzik ◽

Wilkojc ◽

Kwiatkowska-Kopka ◽

Sklodowska

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

High Throughput Sequencing ◽

Extreme Environment ◽

Microbial Colonization ◽

Marker Genes ◽

Lime Mortar ◽

Preventive Actions ◽

Important Challenge ◽

Cultural Heritage Objects

Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e. g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.

Download Full-text

Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0412 ◽

2020 ◽

Vol 66 (4) ◽

pp. 263-273

Author(s):

Julien Saavedra-Lavoie ◽

Anne de la Porte ◽

Sarah Piché-Choquette ◽

Claude Guertin ◽

Philippe Constant

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Co Oxidation ◽

Soil Microbial Communities ◽

Amplicon Sequencing ◽

Oxidative Capacity ◽

Rrna Gene ◽

Soil Microbial Diversity ◽

Soil Microcosms ◽

Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

Download Full-text

H. pylori Eradication Treatment Alters Gut Microbiota and GLP-1 Secretion in Humans

Journal of Clinical Medicine ◽

10.3390/jcm8040451 ◽

2019 ◽

Vol 8 (4) ◽

pp. 451 ◽

Cited By ~ 11

Author(s):

Isabel Cornejo-Pareja ◽

Gracia Martín-Núñez ◽

M. Roca-Rodríguez ◽

Fernando Cardona ◽

Leticia Coin-Aragüez ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Carbohydrate Metabolism ◽

Eradication Therapy ◽

Amplicon Sequencing ◽

Antibiotic Use ◽

Metabolic Disturbances ◽

Bifidobacterium Adolescentis ◽

16S Rrna Amplicon Sequencing ◽

H Pylori

Changes in the intestinal microbial community and some metabolic disturbances, including obesity and type2 diabetes, are related. Glucagon-like peptide-1 (GLP-1) regulates glucose homeostasis. Microbiota have been linked to incretin secretion. Antibiotic use causes changes in microbial diversity and composition. Our aim was to evaluate the relationship between microbiota changes and GLP-1 secretion. A prospective case-control study with a Helicobacter pylori-positive patient model involving subjects under eradication therapy (omeprazole, clarithromycin, and amoxicillin). Forty patients with H. pylori infection and 20 matched participants, but negative for H. pylori antigen. Patients were evaluated before and two months after treatment. We analyzed anthropometric measurements, carbohydrate metabolism, lipid profile, and C-reactive protein. Gut microbiota composition was analyzed through 16S rRNA amplicon sequencing (IlluminaMiSeq). Eradication treatment for H. pylori decreased bacterial richness (Chao1, p = 0.041). Changes in gut microbiota profiles were observed at phylum, family, genus and species levels. GLP-1 secretion and variables of carbohydrate metabolism were improved. Correlations were seen between GLP-1 changes and variations within microbial community abundances, specifically Bifidobacterium adolescentis, the Lachnobacterium genus, and Coriobacteriaceae family. A conventional treatment to eradicate H. pylori could improve carbohydrate metabolism possibly in relation with an increase in GLP-1 secretion. GLP-1 secretion may be related to alterations in intestinal microbiota, specifically Lachnobacterium, B. adolescentis and Coriobacteriaceae.

Download Full-text

Analysis of Microbial Diversity and Variation Law During Xiaoqu Baijiu Fermentation using High-throughput Sequencing Technology

10.21203/rs.3.rs-434877/v1 ◽

2021 ◽

Author(s):

Qing Wang ◽

Xiaoqing Xiang ◽

PengFei Wu ◽

Guoqiang Han

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Sequencing Technology ◽

Theoretical Support ◽

Brewing Process ◽

Dominant Bacteria ◽

Brewing Time

Abstract In this study, high-throughput sequencing (HTS) was used to compare and analyze the microbial diversity and variation law during the brewing process of xiaoqu Baijiu. The results showed that 34 phyla, 378 genera of bacteria and 4 phyla, 32 genera of fungi were detected. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Ascomycota and Bacteroidetes were the dominant groups. During the brewing process of xiaoqu Baijiu, the dominant bacteria were Weissella and unidentified Rickettsiales 2 days before brewing and Lactobacillus 3 days after brewing until the end of brewing. The dominant fungi were Rhizopus, Saccharomyces and Issatchenkia. The relative abundance of Rhizopus decreased with the extension of brewing time, while the relative abundance of Saccharomyces increased and became the dominant bacteria after the second day of brewing. This study revealed the diversity and variation of microbial community in the brewing process of xiaoqu Baijiu, and provide theoretical support and lay the foundation for future study on the contribution of microbial metabolism during brewing of xiaoqu Baijiu, thereby promote the development of xiaoqu baijiu industry.

Download Full-text

Localization of bacterial communities within gut compartments across Cephalotes turtle ants

Applied and Environmental Microbiology ◽

10.1128/aem.02803-20 ◽

2021 ◽

Author(s):

Peter J. Flynn ◽

Catherine L. D’Amelio ◽

Jon G. Sanders ◽

Jacob A. Russell ◽

Corrie S. Moreau

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Digestive Tract ◽

Bacterial Communities ◽

Evolutionary History ◽

Amplicon Sequencing ◽

Caste Differentiation ◽

Animal Group ◽

16S Rrna Amplicon Sequencing ◽

Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

Download Full-text

Protecting Thermally Hydrolyzed Biosolids from Pathogenic Bacterial Growth by Addition of Compost

Waste and Biomass Valorization ◽

10.1007/s12649-020-01300-1 ◽

2020 ◽

Author(s):

Oda K. Svennevik ◽

Kjell R. Jonassen ◽

Kine Svensson ◽

Live H. Hagen ◽

Bjørge Westereng ◽

...

Keyword(s):

Escherichia Coli ◽

Microbial Community ◽

Bacterial Population ◽

Amplicon Sequencing ◽

Thermal Hydrolysis ◽

Regulatory Requirements ◽

E Coli ◽

16S Rrna Amplicon Sequencing ◽

Agricultural Application ◽

Hydrolysis Process

Abstract Sludge biosolids for agricultural application represent a valuable fertilizer but also a health risk unless pathogens are effectively reduced, and recontamination controlled. The Post Anaerobic Digestion Thermal Hydrolysis Process (Post-AD THP) is gaining interest due to improved dewaterability, reducing the volume and thus transportation costs of biosolids. However, Post-AD THP results in sterile biosolids easily exposed to recontamination by pathogens due to the lack of microbial competitors. In theory, this could be suppressed by establishing a competing community of harmless bacteria. The theory was tested by monitoring the abundance of Escherichia coli (viable counts) and gene abundance (ddPCR) in wastewater recontaminated Post-AD THP biosolids, with and without addition of compost. Respiration, total bacterial population and bacterial diversity (16S rRNA amplicon sequencing) were used to monitor the microbial community. Biosolids from the regulatory approved methods thermophilic AD (TAD) and Pre-AD THP were tested in parallel for comparison. The results demonstrated that regulatory requirements can be reached by storing the TAD and Pre-AD THP biosolids for 3 days after recontamination and the Post-AD THP biosolids for more than 13 days. However, addition of compost suppressed growth of E. coli in Post-AD THP biosolids, reducing the time to comply with regulative requirements. In conclusion, pathogen growth in Post-AD THP biosolids can be controlled by inoculation with compost. Graphical abstract

Download Full-text