scholarly journals Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif

mBio ◽  
2021 ◽  
Author(s):  
J. Goordial ◽  
T. D’Angelo ◽  
J. M. Labonté ◽  
N. J. Poulton ◽  
J. M. Brown ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Oceanic Lithosphere ◽  
Global Scale ◽  
Nutrient Cycles ◽  
Subsurface Sediment ◽  
Shallow Subsurface ◽  
Low Concentrations ◽  
Atlantis Massif ◽  
And Function

The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

scholarly journals Shallow Subsurface Sediment Characteristics of Northern Obira Coastal Based on Georadar Facies Interpretation

2021 ◽  
Vol 750 (1) ◽  
pp. 012012
Author(s):  
B Sugiarto ◽  
F B Prasetyo ◽  
M Zulfikar ◽  
G Latuputty ◽  
R Zuraida ◽  
...  
Keyword(s):  
Sediment Characteristics ◽  
Subsurface Sediment ◽  
Shallow Subsurface

A Crucial Role for Diet in the Relationship Between Gut Microbiota and Cardiometabolic Disease

2020 ◽  
Vol 71 (1) ◽  
pp. 149-161 ◽  
Author(s):  
Ilias Attaye ◽  
Sara-Joan Pinto-Sietsma ◽  
Hilde Herrema ◽  
Max Nieuwdorp
Keyword(s):  
Gut Microbiota ◽  
Global Scale ◽  
Cardiometabolic Disease ◽  
Microbiota Composition ◽  
Dietary Interventions ◽  
Fermentable Carbohydrates ◽  
Cost Efficient ◽  
And Function ◽  
Gut Microbiota Composition

Cardiometabolic disease (CMD), such as type 2 diabetes mellitus and cardiovascular disease, contributes significantly to morbidity and mortality on a global scale. The gut microbiota has emerged as a potential target to beneficially modulate CMD risk, possibly via dietary interventions. Dietary interventions have been shown to considerably alter gut microbiota composition and function. Moreover, several diet-derived microbial metabolites are able to modulate human metabolism and thereby alter CMD risk. Dietary interventions that affect gut microbiota composition and function are therefore a promising, novel, and cost-efficient method to reduce CMD risk. Studies suggest that fermentable carbohydrates can beneficially alter gut microbiota composition and function, whereas high animal protein and high fat intake negatively impact gut microbiota function and composition. This review focuses on the role of macronutrients (i.e., carbohydrate, protein, and fat) and dietary patterns (e.g., vegetarian/vegan and Mediterranean diet) in gut microbiota composition and function in the context of CMD.

scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

scholarly journals Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure

2020 ◽  
Author(s):  
Tianming Yao ◽  
Ming-Hsu Chen ◽  
Stephen R. Lindemann
Keyword(s):  
Microbial Diversity ◽  
Structural Complexity ◽  
Structure And Function ◽  
Microbial Consortia ◽  
Carbohydrate Structure ◽  
High Dilution ◽  
Chemical Complexity ◽  
Metabolic Interactions ◽  
And Function

ABSTRACTDietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed an in vitro sequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individual’s fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored by Bacteroides ovatus and retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either by Klebsiella pneumoniae or Bifidobacterium sp. and Escherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates.IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fiber’s structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversity in vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.

scholarly journals β-Glucosidase genes differentially expressed during composting

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xinyue Zhang ◽  
Bo Ma ◽  
Jiawen Liu ◽  
Xiehui Chen ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Degradation Process ◽  
Global Scale ◽  
Expression Of Genes ◽  
Glucose Tolerant ◽  
Cooling Phase ◽  
And Function

Abstract Background Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. Results To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. Conclusion Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.

The formation, preservation and seismic signatures of chemical heterogeneities in the lower mantle

2020 ◽  
Author(s):  
Anna J. P. Gülcher ◽  
Maxim D. Ballmer ◽  
Paul J. Tackley ◽  
Paula Koelemeijer
Keyword(s):  
Physical Properties ◽  
Lower Mantle ◽  
Numerical Models ◽  
Bulk Composition ◽  
Oceanic Lithosphere ◽  
Global Scale ◽  
Seismic Velocities ◽  
Mantle Dynamics ◽  
Wide Range ◽  
Scientific Challenge

<p>Despite stirring by vigorous convection over billions of years, the Earth’s lower mantle appears to be chemically heterogeneous on various length scales. Constraining this heterogeneity is key for assessing Earth’s bulk composition and thermochemical evolution, but remains a scientific challenge that requires cross-disciplinary efforts. On scales below ~1 km, the concept of a “marble cake” mantle has gained wide acceptance, emphasising that recycled oceanic lithosphere, deformed into streaks of depleted and enriched compositions, makes up much of the mantle. On larger scales (10s-100s of km), compositional heterogeneity may be preserved by delayed mixing of this marble cake with either intrinsically-dense or intrinsically-strong materials. Intrinsically dense materials may accumulate as piles at the core-mantle boundary, while intrinsically viscous domains (e.g., enhanced in the strong mineral bridgmanite) may survive as “blobs” in the mid-mantle for large timescales, such as plums in the mantle “plum pudding”<sup>1,2</sup>. While many studies have explored the formation and preservation of either intrinsically-dense (recycled) or intrinsically-strong (primordial) heterogeneity, only few if any have quantified mantle dynamics in the presence of different types of heterogeneity with distinct physical properties.<span> </span></p><p>To address this objective, we use state-of-the-art 2D numerical models of global-scale mantle convection in a spherical-annulus geometry. We explore the effects of the <em>(i)</em> physical properties of primordial material (density, viscosity), <em>(ii)</em> temperature/pressure dependency of viscosity, <em>(iii)</em> lithospheric yielding strength, and <em>(iv)</em> Rayleigh number on mantle dynamics and mixing. Models predict that primordial heterogeneity is preserved in the lower mantle over >4.5 Gyr as discrete blobs for high intrinsic viscosity contrast (>30x) and otherwise for a wide range of parameters. In turn, recycled oceanic crust is preserved in the lower mantle as “marble cake” streaks or piles, particularly in models with a relatively cold and stiff mantle. Importantly, these recycled crustal heterogeneities can co-exist with primordial blobs, with piles often tending to accumulate beneath the primordial domains. This suggests that the modern mantle may be in a hybrid state between the “marble cake” and “plum pudding” styles.<span> </span></p><p>Finally, we put our model predictions in context with recent discoveries from seismology. We calculate synthetic seismic velocities from predicted temperatures and compositions, and compare these synthetics to tomography models, taking into account the limited resolution of seismic tomography. Convection models including preserved bridgmanite-enriched domains along with recycled piles have the potential of reconciling recent seismic observations of lower-mantle heterogeneity<sup>3</sup> with the geochemical record from ocean-island basalts<sup>4,5</sup>, and are therefore relevant for assessing Earth’s bulk composition and long-term evolution.<span> </span></p><p><sup>1</sup> Ballmer et al. (2017), <em>Nat. Geosci</em>., 10.1038/ngeo2898<br><sup>2</sup> Gülcher et al. (in review), <em>EPSL</em>: Variable dynamic styles of primordial heterogeneity preservation in Earth’s lower mantle <br><sup>3</sup> Waszek et al. (2018), <em>Nat. Comm., </em>10.1038/s41467-017-02709-4 <br><sup>4</sup> Hofmann (1997), <em>Nature, </em>10.1038/385219a0; <br><sup>5</sup> Mundl et al. (2017), <em>Science, </em>10.1126/science.aal4179</p>

Expression and function of KCNH2 (HERG) in the human jejunum

2003 ◽  
Vol 284 (6) ◽  
pp. G883-G895 ◽  
Author(s):  
A. M. Farrelly ◽  
S. Ro ◽  
B. P. Callaghan ◽  
M. A. Khoyi ◽  
N. Fleming ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Interstitial Cells Of Cajal ◽  
Circular Muscle ◽  
Slow Waves ◽  
Enteric Neurons ◽  
Longitudinal Smooth Muscle ◽  
Low Concentrations ◽  
Pair Sequence ◽  
And Function ◽  
Cells Of Cajal

Previous studies suggest that ether-a-go-go related gene (ERG) KCNH2 potassium channels contribute to the control of motility patterns in the gastrointestinal tract of animal models. The present study examines whether these results can be translated into a role in human gastrointestinal muscles. Messages for two different variants of the KCNH2 gene were detected: KCNH2 V1 human ERG (HERG) (28) and KCNH2 V2 (HERGUSO) (13). The amount of V2 message was greater than V1 in both human jejunum and brain. The base-pair sequence that gives rise to domains S3– S5 of the channel was identical to that previously published for human KCNH2 V1 and V2. KCNH2 protein was detected immunohistochemically in circular and longitudinal smooth muscle and enteric neurons but not in interstitial cells of Cajal. In the presence of TTX (10−6 M), atropine (10−6M). and l-nitroarginine (10−4 M) human jejunal circular muscle strips contracted phasically (9 cycles/min) and generated slow waves with superimposed spikes. Low concentrations of the KCNH2 blockers E-4031 (10−8 M) and MK-499 (3 × 10−8 M) increased phasic contractile amplitude and the number of spikes per slow wave. The highest concentration of E-4031 (10−6 M) produced a 10–20 mV depolarization, eliminated slow waves, and replaced phasic contractions with a small tonic contracture. E-4031 (10−6 M) did not affect [14C]ACh release from enteric neurons. We conclude that KCNH2 channels play a fundamental role in the control of motility patterns in human jejunum through their ability to modulate the electrical behavior of smooth muscle cells.

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