scholarly journals Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Vadim Schütz ◽  
Katharina Frindte ◽  
Jiaxin Cui ◽  
Pengfan Zhang ◽  
Stéphane Hacquard ◽  
...  
Keyword(s):  
Community Composition ◽  
Relative Abundance ◽  
Soil Bacteria ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Plant Secondary Metabolites ◽  
Sequence Variant ◽  
Plant Metabolites ◽  
Isolation And Characterization ◽  
Mutual Adaptation

Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of field soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the community composition from phylum to amplicon sequence variant (ASV) level. Alpha diversity was significantly reduced by BOA or quercetin, but not by gramine. BOA treatment caused a decrease of the relative abundance of 11 ASVs, while only 10 ASVs were increased. Gramine or quercetin treatment resulted in the increase in relative abundance of many more ASVs (33 or 38, respectively), most of them belonging to the Proteobacteria. Isolation and characterization of cultivable bacteria indicated an enrichment in Pseudarthrobacter or Pseudomonas strains under BOA/quercetin or BOA/gramine treatments, respectively. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a predominantly inhibitory effect, with only few genera being able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, BOA or gramine biosynthesis, which have evolved in different barley species, is accompanied with the association of distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.

scholarly journals Differential impact of plant secondary metabolites on the soil microbiota

2021 ◽  
Author(s):  
Vadim Schütz ◽  
Katharina Frindte ◽  
Jiaxin Cui ◽  
Pengfan Zhang ◽  
Stéphane Hacquard ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Soil Bacteria ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Plant Secondary Metabolites ◽  
Alpha Diversity ◽  
Inhibitory Effect ◽  
Plant Metabolites ◽  
Isolation And Characterization ◽  
Mutual Adaptation

AbstractPlant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the composition of bacterial taxa on the phylum and genus levels. Alpha diversity was significantly altered by BOA or quercetin, but not by gramine. BOA treatment caused an increase in the relative abundances of only four genera, three of them belonging to the Actinobacteriota. Gramine or quercetin treatment resulted in the increase in relative abundance of 13 or 14 genera, respectively, most of them belonging to the Proteobacteria. The relative abundance of 22 genera was decreased after BOA treatment, 16 of which were also decreased by gramine or quercetin. Isolation and characterization of cultivable bacterial indicated an enrichment in specific Arthrobacter or Pseudomonas strains. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a broad-spectrum inhibitory effect, with only few genera able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, benzoxazolinone or gramine biosynthesis which have evolved in different barley species, is accompanied with the association with distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.

Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

2021 ◽  
Author(s):  
Amandine Erktan ◽  
MD Ekramul Haque ◽  
Jérôme Cortet ◽  
Paul Henning Krogh ◽  
Stefan Scheu
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Trophic Interactions ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Trophic Levels ◽  
Soil Matrix ◽  
Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 µm) usually are more stable than macroaggregates (> 250 µm) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 µm – 2mm) and microaggregates (50 – 250 µm). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

scholarly journals PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 293-294
Author(s):  
Camila S Marcolla ◽  
Benjamin Willing
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Poultry Production ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

Permafrost-derived dissolved organic matter character controls microbial community composition in Arctic coastal waters

2021 ◽  
Author(s):  
Anders Dalhoff Bruhn ◽  
Colin A. Stedmon ◽  
Jérôme Comte ◽  
Atsushi Matsuoka ◽  
Neik Jesse Speetjens ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
The Arctic ◽  
Glacial Deposit ◽  
Deposit Type ◽  
Lacustrine Deposit

<p>Climate warming is accelerating erosion rates along permafrost-dominated Arctic coasts. To study the impact of erosion on marine microbial community composition and growth in the Arctic coastal zone, dissolved organic matter (DOM) from three representative glacial landscapes (fluvial, lacustrine and moraine) along the Yukon coastal plain, are provided as substrate to marine bacteria using a chemostat setup. Our results indicate that chemostat cultures with a flushing rate of approximately a day provide comparable DOM bioavailability estimates to those from bottle experiments lasting weeks to months. DOM composition (inferred from UV-Visible spectroscopy) and biodegradability (inferred from DOC concentration, bacterial production and respiration) significantly differed between the three glacial deposit types. DOM from fluvial and moraine deposit types shows more terrestrial characteristics with lower aromaticity (S<sub>R</sub>: 0.63 (±0.02), SUVA<sub>254</sub>: 1.65 (±0.06) respectively S<sub>R</sub>: 0.68 (±0.00), SUVA<sub>254</sub>: 1.17 (±0.06)) compared to the lacustrine deposit type (S<sub>R</sub>: 0.71 (±0.02), SUVA<sub>254</sub>: 2.15 (±0.05)). The difference in composition of DOM corresponds with the development of three distinct microbial communities, with a dominance of Alphaproteobacteria for fluvial and lacustrine deposit types (relative abundance 0.67 and 0.87 respectively) and a dominance of Gammaproteobacteria for moraine deposit type (relative abundance 0.88). Bacterial growth efficiency (BGE) is 66% for moraine-derived DOM, while 13% and 28% for fluvial-derived and lacustrine-derived DOM respectively. The three microbial communities therefore differ in their net effect on DOM utilization. The higher BGE value for moraine-derived DOM was found to be due to a larger proportion of labile colourless DOM. The results from this study, therefore indicate a substrate control of marine microbial community composition and activities, suggesting that the effect of permafrost thaw and erosion in the Arctic coastal zone will depend on subtle differences in DOM related to glacial deposit types. These differences further determines the speed and extent of DOM mineralization and thereby carbon channelling into biomass in the microbial food web. We therefore conclude that marine microbes strongly respond to the input of terrestrial DOM released during coastal erosion of Arctic glacial landscapes.</p>

scholarly journals Changes in Microbial Community Composition and Geochemistry during Uranium and Technetium Bioimmobilization

2007 ◽  
Vol 73 (18) ◽  
pp. 5885-5896 ◽  
Author(s):  
Mandy M. Michalsen ◽  
Aaron D. Peacock ◽  
Anne M. Spain ◽  
Amanda N. Smithgal ◽  
David C. White ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Fatty Acid Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Significant Difference ◽  
And Control

ABSTRACT In a previous column study, we investigated the long-term impact of ethanol additions on U and Tc mobility in groundwater (M. M. Michalsen et al., Environ. Sci. Technol. 40:7048-7053, 2006). Ethanol additions stimulated iron- and sulfate-reducing conditions and significantly enhanced U and Tc removal from groundwater compared to an identical column that received no ethanol additions (control). Here we present the results of a combined signature lipid and nucleic acid-based microbial community characterization in sediments collected from along the ethanol-stimulated and control column flow paths. Phospholipid fatty acid analysis showed both an increase in microbial biomass (∼2 orders of magnitude) and decreased ratios of cyclopropane to monoenoic precursor fatty acids in the stimulated column compared to the control, which is consistent with electron donor limitation in the control. Spatial shifts in microbial community composition were identified by PCR-denaturing gradient gel electrophoresis analysis as well as by quantitative PCR, which showed that Geobacteraceae increased significantly near the stimulated-column outlet, where soluble electron acceptors were largely depleted. Clone libraries of 16S rRNA genes from selected flow path locations in the stimulated column showed that Proteobacteria were dominant near the inlet (46 to 52%), while members of candidate division OP11 were dominant near the outlet (67%). Redundancy analysis revealed a highly significant difference (P = 0.0003) between microbial community compositions within stimulated and control sediments, with geochemical variables explaining 68% of the variance in community composition on the first two canonical axes.

scholarly journals Variation of Gut Microbiome in Free-Ranging Female Tibetan Macaques (Macaca thibetana) across Different Reproductive States

Animals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 39
Author(s):  
Binghua Sun ◽  
Xiaojuan Xu ◽  
Yingna Xia ◽  
Yumei Cheng ◽  
Shuxin Mao ◽  
...  
Keyword(s):  
Community Composition ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Potential Functions ◽  
Rrna Gene ◽  
Macaca Thibetana ◽  
Wild Female ◽  
Pregnancy And Lactation

The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Changes in the gut microbiome may lead to varying nutrient utilizing efficiency in pregnant and lactating female primates. In this study, we examined variation in the gut bacterial community composition of wild female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). Fecal samples (n = 25) were collected from ten adult females harvested across different reproductive states. Gut microbial community composition and potential functions were assessed using 16 S rRNA gene sequences. We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, the relative abundance of predicted functional genes of several metabolic pathways related to host’s energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were enriched in pregnancy and lactation. Our findings suggest that changes in the gut microbiome may play an important role in meeting the energetic needs of pregnant and lactating Tibetan macaques. Future studies of the “microbial reproductive ecology” of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted.

scholarly journals Soil microbial respiration, biomass carbon and community composition data induced by substrate quality from an agricultural grassland

2021 ◽  
Author(s):  
Vito Abbruzzese
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Respiration ◽  
Phospholipid Fatty Acid ◽  
Total Phospholipid ◽  
Microbial Community Composition ◽  
Microbial Biomass C ◽  
Co2 Efflux ◽  
Silty Clay ◽  
Substrate Quality

The data presented here are related to the research article entitled ‘Effects ofsubstrate quality on carbon partitioning and microbial community composition in soil from an agricultural grassland’ [1]. Data illustrate cumulative CO2 efflux, microbial biomass C (Cmic), priming effect expressed as priming index (PI) and total phospholipid fatty acid (PLFA) profiles. The data were measured during four soil laboratory incubations using a silty clay loam soil under permanent grassland from May until August 2015. The soil was treated with carbohydrates of different complexity (glucose, glucose-6-phosphate (G6P) or cellulose) alone or in conjunction with livestock slurry amended or non-amended with a biological additive. Our data may be of great significance for further studies on microbial respiration and biosynthesis, and microbial community structure following slurry application to soil, alongside the potential beneficial effects of the addition of slurry amended with biological additives.

scholarly journals Switch of fungal to bacterial degradation in natural, drained and rewetted oligotrophic peatlands reflected in δ<sup>15</sup>N and fatty acid composition

2020 ◽  
Author(s):  
Miriam Groß-Schmölders ◽  
Pascal von Sengbusch ◽  
Jan Paul Krüger ◽  
Kristy Woodard ◽  
Axel Birkholz ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Microbial Community ◽  
Stable Isotope ◽  
Community Composition ◽  
Turning Point ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Microscopic Analysis ◽  
Bacterial Degradation ◽  
Ecosystem Functions

Abstract. During the last centuries major parts of European peatlands were degraded along with drainage and land use changes. Peatland biodiversity and essential ecosystem functions (e.g. flood prevention, groundwater purification and CO2 sink) were dramatically impaired. Moreover, climate change threatens peatlands in the near future. Increasing pressure to peatland ecosystems calls for a more cost-efficient method to indicate the current state of peatlands and the success of restoration effort. Metabolism processes in peatland soils are imprinted in stable isotope signatures due to differences in microorganism communities and their metabolic pathways. Therefore we hypothesize that depth profiles of nitrogen stable isotope values provide a promising opportunity to detect peatland decomposition or restoration. We studied five peatlands: Degerö Stormyr (Northern Sweden), Lakkasuo (Central Finland) and three mires in the Black Forest (Southern Germany). At all locations cores were taken from adjacent drained (or rewetted) and natural sites to identify δ15N trends that could indicate changes due to drainage and restoration. At all drained (and rewetted) sites we found a distinct peak (turning point) of the δ15N values in the center of the drained horizon. To verify our interpretation δ13C, the C / N ratio and the bulk density were measured and a microscopic analysis of the macro residuals in the peat cores was made. In addition we did a phospholipid fatty acid (PLFAs) analysis to link our results to microbial community composition. We distinguished between fungal and bacterial-derived PLFAs. In accordance with other studies, our results suggest, that fungi dominate the microbial metabolism in the upper, aerobic peat horizon. This is reflected by depleted δ15N values. Downwards the drained horizon conditions slowly switch to oxygen limitation. In consequence fungal-derived PLFAs decreases whereas bacterial-derived PLFAs are rising. The highest diversity of microbial-derived PLFAs is indicated by the δ15N turning point. Below the δ15N turning point, oxygen is increasingly limited and concentrations of all microbial-derived PLFAs are decreasing down to the onset of the permanently waterlogged, anaerobic horizon. Peatland cores with restoration success show, above the formerly drainage-affected horizon, again no depth trend of the isotopic values. Hence, we conclude that δ15N stable isotope values reflect microbial community composition, which differ between drained and natural peatlands.

scholarly journals Irrigation Water Chemistry: Impact on Microbial Community Composition and Biogeochemical Leaching under Perennial Ryegrass (Lolium perenne [L])

ISRN Ecology ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Leon C. Holgate ◽  
Jacqueline A. Aitkenhead-Peterson ◽  
Terry J. Gentry
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Lolium Perenne ◽  
Relative Abundance ◽  
Tap Water ◽  
Microbial Community Composition ◽  
Rain Water ◽  
Gram Positive ◽  
Grey Water ◽  
Gram Negative

Greywater recycling and rain water harvesting for irrigating urban and suburban landscapes may reduce the use of potable water in arid and subtropical climates but affect soil microbial community composition and biogeochemical cycling. Municipal tap water, greywater, and harvested rain water were used to irrigate (Lolium perenne L.) planted in a constructed soil over a 20 week period. Irrigation with grey water significantly increased the relative abundance of gram-positive biomarkers ANTEISO 15 : 0, ISO 17 : 1G, gram-negative biomarkers 19 : 0 CYCLO c11-12 and bacterial biomarker 18 : 0 () relative to irrigation with harvested rain water. Significant decreases were observed in the relative abundance of gram-positive biomarker 16 : 0, gram-negative biomarker 16 : 1 ω7c, both fungi biomarkers (18 : 2 ω6c and 18 : 1 ω9c) in soils irrigated with greywater (). Dissolved organic carbon losses from soil were a significant two-to-four times greater from soils irrigated with municipal tap water and greywater relative to soils irrigated with harvested rain water (). This study highlights the effect that municipal tap water and grey water may have on microbial community composition and soil nutrient dynamics under irrigated turf grass.

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