scholarly journals Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone

2018 ◽  
Author(s):  
Emily B. Graham ◽  
Alex R. Crump ◽  
David W. Kennedy ◽  
Evan Arntzen ◽  
Sarah Fansler ◽  
...  
Keyword(s):  
Organic Matter ◽  
Metabolic Pathways ◽  
Hyporheic Zone ◽  
Microbiome Composition ◽  
C Pools ◽  
Hyporheic Zones ◽  
Organic Matter Processing ◽  
Or Gene ◽  
And Function ◽  
Low Activity

AbstractBiogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi ‘omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments through a shift towards carbohydrate-utilizing metabolic pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C content only (explaining 67% vs. 42% of variation), and bulk C did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.

More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

2019 ◽  
Vol 50 (1) ◽  
pp. 145-168 ◽  
Author(s):  
Muhammad Saleem ◽  
Jie Hu ◽  
Alexandre Jousset
Keyword(s):  
Plant Growth ◽  
Community Ecology ◽  
Soil Health ◽  
Soil Microbiome ◽  
Sustainable Food ◽  
Microbiome Composition ◽  
Change Context ◽  
Beneficial Traits ◽  
Or Gene ◽  
And Function

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

scholarly journals How Changes in the Nutritional Landscape Shape Gut Immunometabolism

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 823
Author(s):  
Jian Tan ◽  
Duan Ni ◽  
Rosilene V. Ribeiro ◽  
Gabriela V. Pinget ◽  
Laurence Macia
Keyword(s):  
Immune Cells ◽  
Metabolic Pathways ◽  
Immune Cell ◽  
Food Additives ◽  
Cell Activity ◽  
Inflammatory Cells ◽  
Therapeutic Approaches ◽  
Food Antigens ◽  
And Function ◽  
Micro Organisms

Cell survival, proliferation and function are energy-demanding processes, fuelled by different metabolic pathways. Immune cells like any other cells will adapt their energy production to their function with specific metabolic pathways characteristic of resting, inflammatory or anti-inflammatory cells. This concept of immunometabolism is revolutionising the field of immunology, opening the gates for novel therapeutic approaches aimed at altering immune responses through immune metabolic manipulations. The first part of this review will give an extensive overview on the metabolic pathways used by immune cells. Diet is a major source of energy, providing substrates to fuel these different metabolic pathways. Protein, lipid and carbohydrate composition as well as food additives can thus shape the immune response particularly in the gut, the first immune point of contact with food antigens and gastrointestinal tract pathogens. How diet composition might affect gut immunometabolism and its impact on diseases will also be discussed. Finally, the food ingested by the host is also a source of energy for the micro-organisms inhabiting the gut lumen particularly in the colon. The by-products released through the processing of specific nutrients by gut bacteria also influence immune cell activity and differentiation. How bacterial metabolites influence gut immunometabolism will be covered in the third part of this review. This notion of immunometabolism and immune function is recent and a deeper understanding of how lifestyle might influence gut immunometabolism is key to prevent or treat diseases.

Enzyme Activities of NADPH-Forming Metabolic Pathways in Normal and Leukemic Leukocytes

1975 ◽  
Vol 21 (7) ◽  
pp. 880-883 ◽  
Author(s):  
Francesco Belfiore ◽  
Vito Borzi ◽  
Luigi Lo Vecchio ◽  
Elena Napoli ◽  
Agata M Rabuazzo
Keyword(s):  
Malate Dehydrogenase ◽  
Metabolic Pathways ◽  
Normal Subjects ◽  
Atp Citrate Lyase ◽  
Phosphogluconate Dehydrogenase ◽  
Myelocytic Leukemia ◽  
Citrate Lyase ◽  
Enzymatic Characteristic ◽  
I Cells ◽  
Low Activity

Abstract With respect to the enzymes of NADPH-forming metabolic pathways in human leukocytes: (a) Glucose-6phosphate dehydrogenase and phosphogluconate dehydrogenase (decarboxylating) were less active in leukocytes (mostly myeloblasts) from eight patients with acute myeloblastic leukemia (I) than in leukocytes (mostly granulocytes) from 16 normal subjects (II) or 16 patients with chronic myelocytic leukemia (III). (b) Of the enzymes of the citrate cleavage pathway, ATP citrate lyase and malate dehydrogenase (decarboxylating) (NADP+) were virtually absent in the cells studied. (c) Isocitrate dehydrogenase (NADP+), aspartate aminotransferase, and alanine aminotransferase, which, together with the much more active malate dehydrogenase, constitute a newly proposed NADPH-forming metabolic cycle, showed a higher activity in I than in II or III, and therefore could compensate, as concerns NADPHgeneration, for the low activity of pentose cycle dehydrogenases. We are not sure whether the enzymatic characteristic of I cells is attributable to their immaturity or to their leukemic nature.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

Effects of riffle–step restoration on hyporheic zone chemistry in N-rich lowland streams

2006 ◽  
Vol 63 (1) ◽  
pp. 120-133 ◽  
Author(s):  
Tamao Kasahara ◽  
Alan R Hill
Keyword(s):  
Urban Areas ◽  
Hyporheic Zone ◽  
Stream Water ◽  
Ion Concentration ◽  
Hyporheic Exchange ◽  
Ecosystem Functions ◽  
Exchange Flow ◽  
Nutrient Inputs ◽  
Lowland Streams ◽  
Hyporheic Zones

Stream restoration projects that aim to rehabilitate ecosystem health have not considered surface–subsurface linkages, although stream water and groundwater interaction has an important role in sustaining stream ecosystem functions. The present study examined the effect of constructed riffles and a step on hyporheic exchange flow and chemistry in restored reaches of several N-rich agricultural and urban streams in southern Ontario. Hydrometric data collected from a network of piezometers and conservative tracer releases indicated that the constructed riffles and steps were effective in inducing hyporheic exchange. However, despite the use of cobbles and boulders in the riffle construction, high stream dissolved oxygen (DO) concentrations were depleted rapidly with depth into the hyporheic zones. Differences between observed and predicted nitrate concentrations based on conservative ion concentration patterns indicated that these hyporheic zones were also nitrate sinks. Zones of low hydraulic conductivity and the occurrence of interstitial fines in the restored cobble-boulder layers suggest that siltation and clogging of the streambed may reduce the downwelling of oxygen- and nitrate-rich stream water. Increases in streambed DO levels and enhancement of habitat for hyporheic fauna that result from riffle–step construction projects may only be temporary in streams that receive increased sediment and nutrient inputs from urban areas and croplands.

scholarly journals Patterns and trends of organic matter processing and transport: Insights from the US Long-Term Ecological Research network

2021 ◽  
pp. 100025
Author(s):  
Tamara K. Harms ◽  
Peter M. Groffman ◽  
Lihini Aluwihare ◽  
Chris Craft ◽  
William R Wieder ◽  
...  
Keyword(s):  
Organic Matter ◽  
Research Network ◽  
Ecological Research ◽  
The Us ◽  
Long Term Ecological Research ◽  
Organic Matter Processing

Functional role of earthworms to control the hydraulic conductivity of constructed wetlands 

2021 ◽  
Author(s):  
Océane Gilibert ◽  
Dan Tam Costa ◽  
Sabine Sauvage ◽  
Didier Orange ◽  
Yvan Capowiez ◽  
...  
Keyword(s):  
Organic Matter ◽  
Hydraulic Conductivity ◽  
Constructed Wetlands ◽  
Hyporheic Zone ◽  
Riparian Zone ◽  
Water Flux ◽  
Sediment Surface ◽  
Deep Soil ◽  
The Impact ◽  
Organic Matter Input

<p>Wetlands are known for their natural service of water quality regulation. The hyporheic zones of the rivers filter and purify the surface water from the stream and infiltrated waters in soil nearby through the riparian zone. This purification service occurs because of a synergy between the substrate and its biodiversity (including plants, bacteria and other invertebrates). Our study deals with constructed wetlands (CW) as a nature-based solution mimicking wetlands water purification process, to purify wastewaters. The REUSE technology of CW is based on the use of specific layers of gravels and sands inside a close concrete structure, planted with specific sub-aquatic plants, where wastewaters or runoff of stormwaters are introduced to be filtered. The technology of Vertical Flow Constructed Wetlands (VFCW) reproduces the water flux observed in the riparian zone with a gravity flow of water. It is composed of reeds planted on a sandy layer (Ø 0-4 mm) and succession of gravel layers. This substrate can be saturated or unsaturated to reproduce the functioning of the hyporheic zone or the riparian zone respectively. By the time, the substrate is colonized by a community of bacteria producing biofilms which capture the residual organic matter from wastewaters to mineralize them. However, the VFCW substrates tend to clog over time due to the accumulation of organic matter and biofilms. Many studies consider earthworms as one of the solutions to alleviate this clogging, thanks to their burrows recreating macropores and preferential channels which help to improve the dispersion of water into the deep soil. The main goal of this study is to assess the impact of earthworm activities on the hydraulic conductivity of columns composed with the same substrate used in the VFCW. Different densities of earthworms (Eisenia fetida) were introduced (0, 100, 500, 1000 g of earthworms/m²) in these columns to be monitored for 37 days. The hydraulic conductivity was measured every 7 days, aside from day 23 with the addition of 40 g of peat bedding on column surfaces to simulate a high organic matter input. Columns with earthworm density superior to 500 g/m² shows an amelioration of their hydraulic conductivity after 21 days. These densities are also able to restore the hydraulic conductivity of the column in less than 7 days after the setting of clogged condition due to the organic matter input (peat bedding) at the sediment surface. This study showed that the burrowing activity of E. fetida improves the hydraulic flux of a sandy substrate and this impact is dependent on the earthworm density introduced. So, the addition of earthworms in the VFCW could serve as a prevention against clogging.</p>

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

scholarly journals Unlocking Elementary Conversion Modes: ecmtool unveils all capabilities of metabolic networks

2020 ◽  
Author(s):  
Tom J. Clement ◽  
Erik B. Baalhuis ◽  
Bas Teusink ◽  
Frank J. Bruggeman ◽  
Robert Planqué ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Metabolic Networks ◽  
Full Range ◽  
Biotechnological Potential ◽  
Metabolic Network Reconstruction ◽  
And Function ◽  
Multicellular Organisms ◽  
Genome Scale ◽  
Threat Levels ◽  
Experimental Characterisation

AbstractThe metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterisation is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be computed from an organism’s annotated genome using metabolic network reconstruction. However, current computational methods cannot deal with genome-scale metabolic networks. Part of the problem is that these methods aim to enumerate all metabolic pathways, while computation of all (elementally balanced) conversions between nutrients and products would suffice. Indeed, the elementary conversion modes (ECMs, defined by Urbanczik and Wagner) capture the full metabolic capabilities of a network, but the use of ECMs has not been accessible, until now. We extend and explain the theory of ECMs, implement their enumeration in ecmtool, and illustrate their applicability. This work contributes to the elucidation of the full metabolic footprint of any cell.

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