Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

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A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.015328 ◽

2020 ◽

Vol 295 (51) ◽

pp. 17752-17769

Author(s):

Evan M. Glasgow ◽

Elias I. Kemna ◽

Craig A. Bingman ◽

Nicole Ing ◽

Kai Deng ◽

...

Keyword(s):

Substrate Specificity ◽

Protein Design ◽

Plant Biomass ◽

Catalytic Efficiency ◽

Structural Features ◽

Glycoside Hydrolases ◽

Design Strategies ◽

Biomass Hydrolysis ◽

Diverse Range ◽

Broad Specificity

Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)–linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan, and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.

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Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

Journal of Food Protection ◽

10.4315/0362-028x-68.1.40 ◽

2005 ◽

Vol 68 (1) ◽

pp. 40-48 ◽

Cited By ~ 40

Author(s):

ANABELLE MATOS ◽

JAY L. GARLAND

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Dynamics ◽

Community Level ◽

Microbial Consortia ◽

Single Strain ◽

Acridine Orange Staining ◽

Physiological Profiles ◽

Alfalfa Sprouts ◽

Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

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Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PLoS ONE ◽

10.1371/journal.pone.0089531 ◽

2014 ◽

Vol 9 (3) ◽

pp. e89531 ◽

Cited By ~ 25

Author(s):

Magdalena K. Stoeva ◽

Stéphane Aris-Brosou ◽

John Chételat ◽

Holger Hintelmann ◽

Philip Pelletier ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

High Arctic ◽

Polar Desert

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Effect of arbuscular mycorrhizal fungi on plant biomass and the rhizosphere microbial community structure of mesquite grown in acidic lead/zinc mine tailings

The Science of The Total Environment ◽

10.1016/j.scitotenv.2010.11.020 ◽

2011 ◽

Vol 409 (6) ◽

pp. 1009-1016 ◽

Cited By ~ 69

Author(s):

Fernando A. Solís-Domínguez ◽

Alexis Valentín-Vargas ◽

Jon Chorover ◽

Raina M. Maier

Keyword(s):

Community Structure ◽

Microbial Community ◽

Arbuscular Mycorrhizal Fungi ◽

Mine Tailings ◽

Mycorrhizal Fungi ◽

Plant Biomass ◽

Arbuscular Mycorrhizal ◽

Lead Zinc ◽

Zinc Mine ◽

Rhizosphere Microbial Community

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Effect of Microbial Inoculants on Plant Attributes and Nutrients Uptake by Soybean in Vertisols

International Journal of Plant & Soil Science ◽

10.9734/ijpss/2021/v33i1830580 ◽

2021 ◽

pp. 102-109

Author(s):

Sanjeet Kumar ◽

R. K. Sahu ◽

R. K. Thakur ◽

Bablu Yaduwanshi ◽

N. G. Mitra

Keyword(s):

Crop Production ◽

Plant Biomass ◽

Block Design ◽

Soil Health ◽

Microbial Consortia ◽

Microbial Inoculants ◽

Randomized Block Design ◽

Nutrients Uptake ◽

Agricultural Chemistry ◽

Plant Attributes

The present study was carried out during kharif season 2019-20 at the Research Farm, Department of Soil Science & Agricultural Chemistry, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, Madhya Pradesh (INDIA), to assess the effect of microbial inoculants on plant attributes and nutrients uptake by soybean in Vertisols. The experiment was laid out under randomized block design (RBD) with three replications. The 15 treatments comprised of different beneficial microbial consortia in possible combinations applied as seed treatments. The crop was supplemented with recommended dose of fertilizers 20 N : 80 P2O5 : 20 K2O kg ha-1. Besides these, two control plots were maintained as fertilized un-inoculated control (FUI) and unfertilized un-inoculated control (UFUI). The findings revealed that the significant improvement were noticed by the application of consortia NPK+EM+PGPR in plant growth attributes of nodulation at 25, 45 & 65 DAS (71, 70 & 59% respectively), over control (9.5, 33.4 & 34.7 nodule plant-1) and its biomass, (62, 69 & 74% respectively),over the control (0.58, 1.16 & 0.99 g plant-1), plant height at 25, 45 & 65DAS were increased 61, 40, 41% respectively, over the control (16.20, 34.90 and 44.30 cm) and plant biomass, (48, 62 & 53%), over the control 1.67, 4.73 and 6.1 g plant-1. Similarly, nutrient uptake (seed & stover) were also increased at 25, 45 and 65 stages of crop growth, with 36.6, 34.8 & 51.3% in seed and 66.7, 98.2 & 67.2% in straw respectively over the control (98.5, 63.8, 5.2, and 7.4, 24.9 and 44.4 kg ha-1 respectively). Thus, it may be concluded that the consortium of NPK + EM + PGPR was superior for sustainable crop production and soil health.

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Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms

Microorganisms ◽

10.3390/microorganisms9071495 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1495

Author(s):

Tim Piel ◽

Giovanni Sandrini ◽

Gerard Muyzer ◽

Corina P. D. Brussaard ◽

Pieter C. Slot ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Composition ◽

Glycoside Hydrolases ◽

Microbial Community Analysis ◽

Cyanobacterial Blooms ◽

Temporary Increase ◽

Low Concentrations ◽

Harmful Cyanobacterial Blooms

Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning.

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HPLC-analyses of plant biomass hydrolysis and fermentation solutions

Chromatographia ◽

10.1007/bf02262975 ◽

1984 ◽

Vol 18 (8) ◽

pp. 445-448 ◽

Cited By ~ 33

Author(s):

G. Bonn ◽

O. Bobleter

Keyword(s):

Plant Biomass ◽

Biomass Hydrolysis ◽

Hplc Analyses

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Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation

Microbial Ecology ◽

10.1007/s00248-015-0683-7 ◽

2015 ◽

Vol 71 (3) ◽

pp. 616-627 ◽

Cited By ~ 49

Author(s):

Maria Julia de Lima Brossi ◽

Diego Javier Jiménez ◽

Larisa Cortes-Tolalpa ◽

Jan Dirk van Elsas

Keyword(s):

Plant Biomass ◽

Microbial Consortia ◽

Lignocellulose Degradation

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System Performance Corresponding to Bacterial Community Succession after a Disturbance in an Autotrophic Nitrogen Removal Bioreactor

mSystems ◽

10.1128/msystems.00398-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Hsiao-Pei Lu ◽

Yung-Hsien Shao ◽

Jer-Horng Wu ◽

Chih-hao Hsieh

Keyword(s):

Time Series ◽

Microbial Community ◽

System Performance ◽

Time Series Data ◽

Microbial Consortia ◽

Series Data ◽

Resolution Time ◽

Physicochemical Variables ◽

System Functioning ◽

Fine Resolution

ABSTRACT Performance of a bioreactor is affected by complex microbial consortia that regulate system functional processes. Studies so far, however, have mainly emphasized the selective pressures imposed by operational conditions (i.e., deterministic external physicochemical variables) on the microbial community as well as system performance, but have overlooked direct effects of the microbial community on system functioning. Here, using a bioreactor with ammonium as the sole substrate under controlled operational settings as a model system, we investigated succession of the bacterial community after a disturbance and its impact on nitrification and anammox (anaerobic ammonium oxidation) processes with fine-resolution time series data. System performance was quantified as the ratio of the fed ammonium converted to anammox-derived nitrogen gas (N2) versus nitrification-derived nitrate (npNO3−). After the disturbance, the N2/npNO3− ratio first decreased, then recovered, and finally stabilized until the end. Importantly, the dynamics of N2/npNO3− could not be fully explained by physicochemical variables of the system. In comparison, the proportion of variation that could be explained substantially increased (tripled) when the changes in bacterial composition were taken into account. Specifically, distinct bacterial taxa tended to dominate at different successional stages, and their relative abundances could explain up to 46% of the variation in nitrogen removal efficiency. These findings add baseline knowledge of microbial succession and emphasize the importance of monitoring the dynamics of microbial consortia for understanding the variability of system performance. IMPORTANCE Dynamics of microbial communities are believed to be associated with system functional processes in bioreactors. However, few studies have provided quantitative evidence. The difficulty of evaluating direct microbe-system relationships arises from the fact that system performance is affected by convolved effects of microbiota and bioreactor operational parameters (i.e., deterministic external physicochemical forcing). Here, using fine-resolution time series data (daily sampling for 2 months) under controlled operational settings, we performed an in-depth analysis of system performance as a function of the microbial community in the context of bioreactor physicochemical conditions. We obtained statistically evaluated results supporting the idea that monitoring microbial community dynamics could improve the ability to predict system functioning, beyond what could be explained by operational physicochemical variables. Moreover, our results suggested that considering the succession of multiple bacterial taxa would account for more system variation than focusing on any particular taxon, highlighting the need to integrate microbial community ecology for understanding system functioning.

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