scholarly journals Synchrony Degree of Dietary Energy and Nitrogen Release Influences Microbial Community, Fermentation, and Protein Synthesis in a Rumen Simulation System

2020 ◽  
Vol 8 (2) ◽  
pp. 231 ◽  
Author(s):  
Jun Zhang ◽  
Nan Zheng ◽  
Weijun Shen ◽  
Shengguo Zhao ◽  
Jiaqi Wang
Keyword(s):  
Protein Synthesis ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Volatile Fatty Acids ◽  
Bacterial Community Composition ◽  
Simulation System ◽  
Lower Degree ◽  
Ammonia Assimilation ◽  
Nitrogen Release ◽  
Post Feeding

Synchrony of energy and nitrogen release in rumen has been proposed to maximize ruminal microbial fermentation. However, the information regarding bacterial community composition and its metabolism under a higher or lower degree of synchronization is limited. In our study, a 0 to 6 h post-feeding infusion (first half infusion, FHI), 6 to 12 h post-feeding infusion (second half infusion, SHI), and 0 to 12 h post-feeding infusion (continuous infusion, CI) of maltodextrin were used to simulate varying degrees of synchronization of energy and nitrogen release in a rumen simulation system. In addition, the bacterial community, metabolite, enzyme activity, and microbial protein synthesis (MPS) were evaluated. Compared with the FHI and CI, the relative abundance of Fibrobacter, Ruminobacter, BF311, and CF231 decreased in the SHI, but that of Klebsiella and Succinivibrio increased in the SHI. The NH3-N and branched-chain volatile fatty acids were significantly higher, but propionate content and activities of glutamate dehydrogenase (GDH) and alanine dehydrogenase were significantly lower in the SHI than those in the FHI and CI. The SHI had lower MPS and less efficiency of MPS than the FHI and CI, which indicated that the SHI had a lower degree of synchronization. Correlation analysis showed that MPS was positively related to GDH activity and relative abundance of Fibrobacter but negatively related to NH3-N and relative abundance of Klebsiella. Therefore, a higher degree of synchronization of energy and nitrogen release increased MPS partly via influencing the bacterial community, metabolism, and enzyme activities of ammonia assimilation in the in vitro fermenters.

scholarly journals Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

2011 ◽  
Vol 77 (14) ◽  
pp. 4924-4930 ◽  
Author(s):  
Max Kolton ◽  
Yael Meller Harel ◽  
Zohar Pasternak ◽  
Ellen R. Graber ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Systemic Resistance ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Content Type ◽  
Biochar Amendment

ABSTRACTAdding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuumL.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with theProteobacteria,Bacteroidetes,Actinobacteria, andFirmicutesphyla. The relative abundance of members of theBacteroidetesphylum increased from 12 to 30% as a result of biochar amendment, while that of theProteobacteriadecreased from 71 to 47%. TheBacteroidetes-affiliatedFlavobacteriumwas the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (ChitinophagaandCellvibrio, respectively) and aromatic compound degraders (HydrogenophagaandDechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

scholarly journals EFFECT OF SYNCHRONIZATION OF CARBOHYDRATE AND PROTEIN SUPPLY  IN THE SUGARCANE BAGASSE BASED DIET ON MICROBIAL PROTEIN SYNTHESIS IN SHEEP

2016 ◽  
Vol 41 (3) ◽  
pp. 135-144 ◽  
Author(s):  
J. Achmadi ◽  
A. T. Suhada ◽  
L. K. Nuswantara ◽  
F. Wahyono
Keyword(s):  
Protein Synthesis ◽  
Sugarcane Bagasse ◽  
Volatile Fatty Acids ◽  
Ammonia Nitrogen ◽  
Microbial Protein ◽  
Microbial Protein Synthesis ◽  
Synchronization Index ◽  
Ruminal Ph ◽  
Post Feeding

The experimental research was conducted to clarify the effect of synchronization of ruminal carbohydrate and protein releases from sugarcane bagasse based diet (SBBD) on microbial protein synthesis in sheep. The first experiment was the formulation of three SBBD with similar nutrient content but differed in synchronization indexes (namely 0.36; 0.50 and 0.63). The in sacco nutrient degradability coefficient was used to calculate the synchronization index of each feedstuff. The second experiment was determination of post feeding ruminal pH, ruminal concentrations of total volatile fatty acids (TVFA) and ammonia nitrogen (NH3-N), and blood urea nitrogen (BUN) level in sheep fed on experimental SBBD. The third experiment was determination of feed digestibility and estimation of microbial nitrogen synthesis (MNP) on the basis of excreted urinary allantoin. The alteration of dietary synchronization index did not change nutrient intake, but the digestibilities of DM, OM and CP were increased (P<0.05). The post feeding ruminal pH was decreased (P<0.05) but concentrations of post feeding ruminal TVFA and NH3-N, and level of BUN were increased (P<0.05) by the treatment of dietary synchronization index. The treatment of dietary synchronization index improved MNP (P<0.05), although dietary synchronization index at 0.63 lowered the MNP (P<0.05). 

scholarly journals Effects of Different Combinations of Sugar and Starch Concentrations on Ruminal Fermentation and Bacterial-Community Composition in vitro

2021 ◽  
Vol 8 ◽  
Author(s):  
Jia-nan Dong ◽  
Song-ze Li ◽  
Xue Chen ◽  
Gui-xin Qin ◽  
Tao Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Production Rate ◽  
Community Composition ◽  
Relative Abundance ◽  
Dry Matter ◽  
Bacterial Community Composition ◽  
Rumen Fermentation ◽  
Gas Production ◽  
Ruminal Fermentation

High levels of starch is known to have positive effects on both energy supply and milk yield but increases the risk of rumen acidosis. The use of sugar as a non-structural carbohydrate could circumvent this risk while maintaining the benefits, but its effects and that of the simultaneous use of both sugar and starch are not as well-understood. This study aimed to evaluate the effects of different combinations of sugar and starch concentrations on ruminal fermentation and bacterial community composition in vitro in a 4 ×4 factorial experiment. Sixteen dietary treatments were formulated with 4 levels of sugar (6, 8, 10, and 12% of dietary dry matter), and 4 levels of starch (21, 23, 25, and 27% of dietary dry matter). Samples were taken at 0.5, 1, 3, 6, 12, and 24 h after cultivation to determine the disappearance rate of dry matter, rumen fermentation parameters and bacterial community composition. Butyric acid, gas production, and Treponema abundance were significantly influenced by the sugar level. The pH, acetic acid, and propionic acid levels were significantly influenced by starch levels. However, the interactive effect of sugar and starch was only observed on the rate of dry matter disappearance. Furthermore, different combinations of starch and sugar had different effects on volatile fatty acid production rate, gas production rate, and dry matter disappearance rate. The production rate of rumen fermentation parameters in the high sugar group was higher. Additionally, increasing the sugar content in the diet did not change the main phylum composition in the rumen, but significantly increased the relative abundance of Bacteroidetes and Firmicutes phyla, while the relative abundance of Proteobacteria was reduced. At the genus level, the high glucose group showed significantly higher relative abundance of Treponema (P &lt; 0.05) and significantly lower relative abundance of Ruminobacter, Ruminococcus, and Streptococcus (P &lt; 0.05). In conclusion, different combinations of sugar and starch concentrations have inconsistent effects on rumen fermentation characteristics, suggesting that the starch in diets cannot be simply replaced with sugar; the combined effects of sugar and starch should be considered to improve the feed utilization rate.

scholarly journals Regulating Soil Bacterial Diversity, Enzyme Activities and Community Composition Using Residues from Golden Apple Snails

2019 ◽  
Author(s):  
Jiaxin Wang ◽  
Xuening Lu ◽  
Jiaen Zhang ◽  
Guangchang Wei ◽  
Yue Xiong
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Soil Nutrients ◽  
Soil Ph ◽  
Relative Abundance ◽  
Enzyme Activities ◽  
Bacterial Community Composition ◽  
Apple Snail ◽  
Low Levels

AbstractGolden apple snails (GAS) have become a serious pest for agricultural production in Asia. A sustainable method for managing GAS is urgently needed, including potentially using them to produce commercial products. In this study, we evaluate the effects of GAS residues (shell and meat) on soil pH, bacterial diversity, enzyme activities, and other soil characteristics. Results showed that the amendment of GAS residues significantly elevated soil pH (to near-neutral), total organic carbon (TOC) (by 10-134%), NO3-N (by 46-912%), NH4-N (by 18-168%) and total nitrogen (TN) (by 12-132%). Bacterial diversity increased 13% at low levels of amendment and decreased 5% at high levels, because low-levels of GAS residues increased soil pH to near-neutral, while high-levels of amendment substantially increased soil nutrients and subsequently suppressed bacterial diversity. The dominant phyla of bacteria were: Proteobacteria (about 22%), Firmicutes (15-35%), Chloroflexi (12%-22%), Actinobacteria (8%-20%) Acidobacteria, Gemmatimonadetes, Cyanobacteria and Bacterioidetes. The amendment of GAS residues significantly increased the relative abundance of Firmicutes, Gemmatimonadetes, Bacterioidetes and Deinococcus-Thermus, but significantly decreased the relative abundance of Chloroflexi, Actinobacteria, Acidobacteria, Cyanobacteria and Planctomycetes. Our results suggest that GAS residues treatment induces a near-neutral and nutrient-rich soil. In this soil, soil pH may not be the best predictor of bacterial community composition or diversity; rather soil nutrients (ie., NH4-N and NO3-N) and soil TOC showed stronger correlations with bacterial community composition. Overall, GAS residues could replace lime for remediation of acidic and degraded soils, not only to remediate physical soil properties, but also microbial communities.ImportanceThe wide spreading golden apple snail (GAS) is a harmful pest to crop productions and could result in soil and air pollutions after death. In the previous study, we developed a biocontrol method: adding GAS residues to acidic soil to mitigate the living GAS invasion and spread, improve soil quality, and reduce soil and air pollution. However, the effects of GAS residues amendment on bacterial diversity and community still remain unclear. This study provided insights into bacterial diversity and community compositions to facilitate the evaluation of GAS residues application.

scholarly journals The total and active bacterial community of the chlorolichen Cetraria islandica and its response to long-term warming in sub-Arctic tundra

2020 ◽  
Author(s):  
Ingeborg J. Klarenberg ◽  
Christoph Keuschnig ◽  
Denis Warshan ◽  
Ingibjörg Svala Jónsdóttir ◽  
Oddur Vilhelmsson
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Relative Abundance ◽  
Environmental Conditions ◽  
Bacterial Community Composition ◽  
Arctic Tundra ◽  
Amplicon Sequencing ◽  
Total Community ◽  
First Time

AbstractLichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear.We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous ASVs (amplicon sequence variants) taxa could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community.Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.

scholarly journals Resilience of planktonic bacterial community structure in response to short-term weather deterioration during the growing season in an alpine lake

Hydrobiologia ◽  
2019 ◽  
Vol 847 (2) ◽  
pp. 535-548
Author(s):  
Tianli Ma ◽  
Yiming Jiang ◽  
Ali H. A. Elbehery ◽  
Stephan Blank ◽  
Rainer Kurmayer ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Growing Season ◽  
Alpine Lake ◽  
Scaling Analysis ◽  
Short Term ◽  
Cooling Period

AbstractThe disturbing effect of a short-term cooling period during summer on planktonic bacterial community structure of an alpine lake was investigated using 16S rDNA pyrosequencing. Proteobacteria, Actinobacteria, and Bacteroidetes constituted the most abundant phyla. During the sampling period (from July to August 2010), a sudden cooling period with high precipitation occurred, as indicated by a decrease in conductivity, calcium, and dissolved organic carbon concentration resulting from increased runoff. The relative abundance of Actinobacteria, Betaproteobacteria, and Cyanobacteria decreased during this short-term cooling period. Instead, a rapid shift from Betaproteobacteria to Gammaproteobacteria occurred, which was mainly caused by an increase of Acinetobacter rhizosphaerae. Soon after the short-term cooling period, warmer weather conditions got re-established and Betaproteobacteria recovered and became again dominant. Non-metric multi-dimensional scaling analysis and Venn diagrams revealed a planktonic bacterial community composition with high similarity at the beginning and the end of the growing season. Air temperature and precipitation were significantly correlated with the observed variation in operational taxonomic unit (OTU) relative abundance. It is concluded that, in response to the short-term cooling period, a distinct planktonic bacterial OTU community developed. It rapidly diminished, however, as summer conditions became re-established, implying the recovery of the original bacterial community structure.

scholarly journals Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection

2021 ◽  
Author(s):  
Milind C. Mutnale ◽  
Gundlapally S. Reddy ◽  
Karthikeyan Vasudevan
Keyword(s):  
Bacterial Community ◽  
Relative Abundance ◽  
Frog Skin ◽  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Skin Microbiome ◽  
Bacterial Phyla ◽  
Frog Species ◽  
Generation Sequencing

AbstractChytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.

scholarly journals Bacterial Community Composition and Chromophoric Dissolved Organic Matter Differs with Culture Time of Skeletonema dohrnii

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 150
Author(s):  
Yang Liu ◽  
Jinjun Kan ◽  
Jing Yang ◽  
Md Abu Noman ◽  
Jun Sun
Keyword(s):  
Organic Matter ◽  
Bacterial Community ◽  
Dissolved Organic Matter ◽  
Community Composition ◽  
Relative Abundance ◽  
Bacterial Community Composition ◽  
Algal Growth ◽  
Chromophoric Dissolved Organic Matter ◽  
Bacterial Phyla ◽  
Culture Time

Skeletonema dohrnii is a common red tide microalgae occurring in the coastal waters and throughout the world. The associated heterotrophic or autotrophic bacteria play vital roles in regulating algal growth, production, and physiology. In this study, we investigated the detailed bacterial community structure associated with the growth of S. dohrnii’s using high-throughput sequencing-based on 16S rDNA. Our results demonstrated that Bacteroidetes (48.04%) and Proteobacteria (40.66%) in all samples accounted for the majority of bacterial populations. There was a significant linear regression relationship between the abundance of bacterial phyla and culture time. Notable shifts in bacterial community composition were observed during algal growth: Flavobacteriales accounted for the vast majority of sequences at the order level. Furthermore, the relative abundance of Rhodobacterales was gradually reduced during the whole growth process of S. dohrnii (0–12 days). However, beyond that, the relative abundance of Marinobacter was slowly increasing. It is noteworthy that five fluorophores (Peaks T1, T2, I, M, and A) were detected during the growth stage of S. dohrnii. The characteristic indexes (fluorescence index, humification index, and biological index) of chromophoric dissolved organic matter (CDOM) also varied with the culture time. In addition, the taxa of bacteria had certain effects on CDOM and they were inextricably linked to each other.

scholarly journals Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra

2019 ◽  
Author(s):  
Ingeborg J. Klarenberg ◽  
Christoph Keuschnig ◽  
Ana J. Russi Colmenares ◽  
Denis Warshan ◽  
Anne D. Jungblut ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
The Arctic ◽  
Gene Copy ◽  
Nitrogen Fixing ◽  
Moss Species

AbstractBacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses, an abundant plant group in Arctic ecosystems, harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of the moss microbiome. Here, we studied the total and potentially active bacterial community associated with Racomitrium lanuginosum, a common moss species in the Arctic, in response to 20-year in situ warming in an Icelandic heathland. We evaluated changes in moss bacterial community composition and diversity. Further, we assessed the consequences of warming for nifH gene copy numbers and nitrogen-fixation rates. Long-term warming significantly changed both the total and the potentially active bacterial community structure. The relative abundance of Proteobacteria increased, while the relative abundance of Cyanobacteria and Acidobacteria decreased. While warming did not affect nitrogen-fixation rates and nifH gene abundance, we did find shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and non-cyanobacterial diazotrophs increasing in relative abundance. Our data suggests that the moss microbial community and the potentially nitrogen-fixing taxa are sensitive to future warming.

scholarly journals Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics

2014 ◽  
Vol 44 (4) ◽  
pp. 922-930 ◽  
Author(s):  
Daniel J. Smith ◽  
Alison C. Badrick ◽  
Martha Zakrzewski ◽  
Lutz Krause ◽  
Scott C. Bell ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Relative Abundance ◽  
Bacterial Community Composition ◽  
Molecular Techniques ◽  
Pulmonary Exacerbation ◽  
Intravenous Antibiotics ◽  
The Impact

Chronic airway infection in adults with cystic fibrosis (CF) is polymicrobial and the impact of intravenous antibiotics on the bacterial community composition is poorly understood. We employed culture-independent molecular techniques to explore the early effects of i.v. antibiotics on the CF airway microbiome.DNA was extracted from sputum samples collected from adult subjects with CF at three time-points (before starting treatment, and at day 3 and day 8–10 of i.v. antibiotics) during treatment of an infective pulmonary exacerbation. Microbial community profiles were derived through analysis of bacterial-derived 16S ribosomal RNA by pyrosequencing and changes over time were compared.59 sputum samples were collected during 24 pulmonary exacerbations from 23 subjects. Between treatment onset and day 3 there was a significant reduction in the relative abundance of Pseudomonas and increased microbial diversity. By day 8–10, bacterial community composition was similar to pre-treatment. Changes in community composition did not predict improvements in lung function.The relative abundance of Pseudomonas falls rapidly in subjects with CF receiving i.v. antibiotic treatment for a pulmonary exacerbation and is accompanied by an increase in overall microbial diversity. However, this effect is not maintained beyond the first week of treatment.

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