scholarly journals Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs

2019 ◽  
Vol 95 (12) ◽  
Author(s):  
Zachary S Cooper ◽  
Josephine Z Rapp ◽  
Shelly D Carpenter ◽  
Go Iwahana ◽  
Hajo Eicken ◽  
...  
Keyword(s):  
Community Structure ◽  
Sea Ice ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Extracellular Polysaccharides ◽  
Rrna Gene ◽  
Alpha And Beta Diversity

ABSTRACT Hypersaline aqueous environments at subzero temperatures are known to be inhabited by microorganisms, yet information on community structure in subzero brines is very limited. Near Utqiaġvik, Alaska, we sampled subzero brines (–6°C, 115–140 ppt) from cryopegs, i.e. unfrozen sediments within permafrost that contain relic (late Pleistocene) seawater brine, as well as nearby sea-ice brines to examine microbial community composition and diversity using 16S rRNA gene amplicon sequencing. We also quantified the communities microscopically and assessed environmental parameters as possible determinants of community structure. The cryopeg brines harbored surprisingly dense bacterial communities (up to 108 cells mL–1) and millimolar levels of dissolved and particulate organic matter, extracellular polysaccharides and ammonia. Community composition and diversity differed between the two brine environments by alpha- and beta-diversity indices, with cryopeg brine communities appearing less diverse and dominated by one strain of the genus Marinobacter, also detected in other cold, hypersaline environments, including sea ice. The higher density and trend toward lower diversity in the cryopeg communities suggest that long-term stability and other features of a subzero brine are more important selective forces than in situ temperature or salinity, even when the latter are extreme.

scholarly journals On giant shoulders: How a seamount affects the microbial community composition of seawater and sponges

2020 ◽  
Author(s):  
Kathrin Busch ◽  
Ulrike Hanz ◽  
Furu Mienis ◽  
Benjamin Müller ◽  
Andre Franke ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Dissolved Inorganic Carbon ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Geographic Location ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
The Arctic ◽  
Rrna Gene

Abstract. Seamounts represent ideal systems to study the influence and interdependency of environmental gradients at a single geographic location. These topographic features represent a prominent habitat for various forms of life, including microbiota and macrobiota, spanning benthic as well as pelagic organisms. While it is known that seamounts are globally abundant structures, it still remains unclear how and to which extend the complexity of the seafloor is intertwined with the local oceanographic mosaic, biogeochemistry and microbiology of a seamount ecosystem. Along these lines, the present study aimed to explore whether and to which extend seamounts can have an imprint on the microbial community composition of seawater and of sessile benthic invertebrates, sponges. For our high-resolution sampling approach of microbial diversity (16S rRNA gene Amplicon sequencing) along with measurements of inorganic nutrients and other biogeochemical parameters, we focused on the Schulz Bank seamount ecosystem, a sponge ground ecosystem which is located on the Arctic Mid-Ocean Ridge. Seawater samples were collected at two sampling depths (mid-water: MW, and near-bed water: BW) from a total of 19 sampling sites. With a clustering approach we defined microbial micro-habitats within the pelagic realm at Schulz Bank, which were mapped onto the seamount's topography, and related to various environmental parameters (such as suspended particulate matter (SPM), dissolved inorganic carbon (DIC), silicate (SiO4−), phosphate (PO43−), ammonia (NH4+), nitrate (NO32−), nitrite (NO2

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

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

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Alicia Balbín-Suárez ◽  
Maik Lucas ◽  
Doris Vetterlein ◽  
Søren J Sørensen ◽  
Traud Winkelmann ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Apple Rootstocks ◽  
Apple Replant Disease ◽  
Alpha And Beta Diversity ◽  
Replant Disease ◽  
Split Root ◽  
And Control

ABSTRACT Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible ‘M26’ apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil–root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil–root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.

scholarly journals Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6172 ◽  
Author(s):  
Yun Kit Yeoh ◽  
Zigui Chen ◽  
Mamie Hui ◽  
Martin C.S. Wong ◽  
Wendy C.S. Ho ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Individual Variation ◽  
Large Scale ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Relative Effect ◽  
Individual Variability ◽  
Rrna Gene ◽  
Sample Collection

Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.

scholarly journals Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sandra A. Appiah ◽  
Christine L. Foxx ◽  
Dominik Langgartner ◽  
Annette Palmer ◽  
Cristian A. Zambrano ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Community Composition ◽  
Gut Microbiome ◽  
Beta Diversity ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Global Changes ◽  
Rrna Gene ◽  
Alpha And Beta Diversity ◽  
Increased Risk

AbstractSevere injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.

scholarly journals Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Derek S Lundberg ◽  
Pratchaya Pramoj Na Ayutthaya ◽  
Annett Strauß ◽  
Gautam Shirsekar ◽  
Wen-Sui Lo ◽  
...  
Keyword(s):  
Community Composition ◽  
Compositional Data ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Microbial Load ◽  
Rrna Gene ◽  
Substantial Cost ◽  
Culture Independent ◽  
Metagenome Sequencing ◽  
Single Amplicon

The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing, add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.

scholarly journals Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Matt Lloyd Jones ◽  
Damian William Rivett ◽  
Alberto Pascual-García ◽  
Thomas Bell
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Focal Point ◽  
Microbial Community Composition ◽  
Common Garden ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Invasion Resistance ◽  
Bacterial Strains ◽  
Microbial Invasion

Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.

scholarly journals Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams

2010 ◽  
Vol 77 (1) ◽  
pp. 302-311 ◽  
Author(s):  
Tatiana A. Vishnivetskaya ◽  
Jennifer J. Mosher ◽  
Anthony V. Palumbo ◽  
Zamin K. Yang ◽  
Mircea Podar ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Inorganic Mercury ◽  
Rrna Gene ◽  
Oak Ridge

ABSTRACTHigh concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, includingProteobacteria(ranging from 22.9 to 58.5% per sample),Cyanobacteria(0.2 to 32.0%),Acidobacteria(1.6 to 30.6%),Verrucomicrobia(3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within theProteobacteriagroup that includes sulfate-reducing bacteria and within theVerrucomicrobiagroup appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on thein situmicrobial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.

scholarly journals Do initial concentration and activated sludge seasonality affect pharmaceutical biodegradation rate constants?

2020 ◽  
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 ◽  
Biodegradation Rate ◽  
Initial Concentration

AbstractPharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs) and biodegradation 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 biodegradation 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 kbvalues were calculated. The biodegradable pharmaceuticals, ranked from high to low biodegradation rates, were acetaminophen, metformin, metoprolol, terbutaline, and phenazone. 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 kbfor some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum different kbvalues were measured, depending on initial concentration. In general, biodegradable compounds had a higher kbwhen the initial concentration was higher. This demonstrates that Michealis-Menten kinetics theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kbin order to reliably predict the fate of pharmaceuticals in the WWTP.

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