Characteristics and selection of efficient lignocellulose degradation microbial community

Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO2 in syntrophic propionate oxidation under elevated partial pressure of CO2 (pCO2). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO2. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO2; however, higher CH4 yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO2: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH4 yield. Our results highlight that limited propionate conversion at elevated pCO2 resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.

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Evaluation of DNA Extraction Methods of Mule Dung

Defence Life Science Journal ◽

10.14429/dlsj.4.14269 ◽

2019 ◽

Vol 4 (3) ◽

pp. 170-174

Author(s):

Rajesh Kumar Vaid ◽

Taruna Anand ◽

Priyanka Batra ◽

Ram Avtar Legha ◽

Bhupendra Nath Tripathi

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

Dna Isolation ◽

Community Analysis ◽

Extraction Methods ◽

Microbial Community Analysis ◽

Animal Dung ◽

Microbial Community Analyses ◽

Dna Extraction Methods ◽

Selection Of

DNA isolation is a critical step in microbial community analysis of animal dung. DNA isolation from mule dung is challenging due to microbial diversity, composition and chemical nature of mule dung. Therefore, selection of an appropriate DNA isolation method is important to analyse the complete microbial diversity. In the current study, we evaluated the DNA isolation from mule dung samples (n=11) using QiAmp Mini stool kit as per manufacturer’s procedure with modifications. The results suggest that modifications in proprietary column based method improved the DNA quality and quantity suitable for mule dung microbial community analyses.

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Effects of Irradiation on Microbial Community Structure in the Yangtze River and Selection of Representative Microorganisms

IOP Conference Series Earth and Environmental Science ◽

10.1088/1742-6596/51/1/012024 ◽

2017 ◽

Vol 51 ◽

pp. 012024 ◽

Cited By ~ 1

Author(s):

J B Song ◽

L P Kuai

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Yangtze River ◽

The Yangtze River ◽

Effects Of Irradiation On ◽

Selection Of

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Understanding the evolution of interspecies interactions in microbial communities

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0256 ◽

2020 ◽

Vol 375 (1798) ◽

pp. 20190256 ◽

Cited By ~ 6

Author(s):

Florien A. Gorter ◽

Michael Manhart ◽

Martin Ackermann

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Interaction Strength ◽

Quantitative Model ◽

Systematic Effect ◽

Interspecies Interactions ◽

Fitness Effects ◽

Indirect Fitness ◽

Beneficial Traits ◽

Selection Of

Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of interspecies interactions in communities. Specifically, we propose that to understand the evolution of interspecies interactions, it is important to distinguish between direct and indirect fitness effects of a mutation. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

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Biodegradation of Lindane and Lignocellulose by Microbial Community

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.113-116.55 ◽

2010 ◽

Vol 113-116 ◽

pp. 55-58

Author(s):

Jian Huang ◽

Chang Li Liu ◽

Zong Jun Cui ◽

Hai Long Shen

Keyword(s):

Mass Spectrometry ◽

Gas Chromatography ◽

Microbial Community ◽

16S Rdna ◽

Organochlorine Pesticide ◽

Clone Library ◽

Lignocellulose Degradation ◽

Bacterial Composition ◽

16S Rdna Clone Library ◽

Rdna Clone

In order to investigate the capability of degradation lindane and lignocellulose of a microbial community, the gas chromatography(GC) was used to determine the concentration of lindane. After 18 days cultured, lindane reduced 6.25% more than the control. And the result of gas chromatography and mass spectrometry (GCMS) showed that the species and quantum of fermentation productions changed much in different phase. In order to determine the bacterial composition of the community, clone library was used to clarified bacterial composition. Constructed 16S rDNA clone library showed 60% closest relative among them were known the detailed information. Strain of closest relative of Clostridium may be main contribute to lignocellulose degradation, and closest relative of Proteobacterium may be the main contribute to degradation organochlorine pesticide (lindane).

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Selection for antibiotic resistance is reduced when embedded in a natural microbial community

10.1101/529651 ◽

2019 ◽

Cited By ~ 4

Author(s):

Uli Klümper ◽

Mario Recker ◽

Lihong Zhang ◽

Xiaole Yin ◽

Tong Zhang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Community ◽

Single Species ◽

Natural Environments ◽

Order Of Magnitude ◽

Natural Microbial Community ◽

Cost Of Resistance ◽

Selection For ◽

The Cost ◽

Selection Of

AbstractAntibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig fecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics: gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration: an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.

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Cellulolytic and Xylanolytic Microbial Communities Associated With Lignocellulose-Rich Wheat Straw Degradation in Anaerobic Digestion

Frontiers in Microbiology ◽

10.3389/fmicb.2021.645174 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mads Borgbjerg Jensen ◽

Nadieh de Jonge ◽

Maja Duus Dolriis ◽

Caroline Kragelund ◽

Christian Holst Fischer ◽

...

Keyword(s):

Microbial Community ◽

Anaerobic Digestion ◽

Microbial Communities ◽

Wheat Straw ◽

Lignocellulosic Biomass ◽

Correlation Method ◽

Amplicon Sequencing ◽

Lignocellulose Degradation ◽

Rrna Gene ◽

Key Species

The enzymatic hydrolysis of lignocellulosic polymers is generally considered the rate-limiting step to methane production in anaerobic digestion of lignocellulosic biomass. The present study aimed to investigate how the hydrolytic microbial communities of three different types of anaerobic digesters adapted to lignocellulose-rich wheat straw in continuous stirred tank reactors operated for 134 days. Cellulase and xylanase activities were monitored weekly using fluorescently-labeled model substrates and the enzymatic profiles were correlated with changes in microbial community compositions based on 16S rRNA gene amplicon sequencing to identify key species involved in lignocellulose degradation. The enzymatic activity profiles and microbial community changes revealed reactor-specific adaption of phylogenetically different hydrolytic communities. The enzymatic activities correlated significantly with changes in specific taxonomic groups, including representatives of Ruminiclostridium, Caldicoprobacter, Ruminofilibacter, Ruminococcaceae, Treponema, and Clostridia order MBA03, all of which have been linked to cellulolytic and xylanolytic activity in the literature. By identifying microorganisms with similar development as the cellulase and xylanase activities, the proposed correlation method constitutes a promising approach for deciphering essential cellulolytic and xylanolytic microbial groups for anaerobic digestion of lignocellulosic biomass.

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Cohesiveness in microbial community coalescence

10.1101/282723 ◽

2018 ◽

Cited By ~ 7

Author(s):

Nanxi Lu ◽

Alicia Sanchez-Gorostiaga ◽

Mikhail Tikhonov ◽

Alvaro Sanchez

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Empirical Work ◽

Invasion Success ◽

Community Members ◽

Interacting Species ◽

Resource Interactions ◽

Different Origins ◽

Microbial Community Assembly ◽

Selection Of

AbstractMicrobial invasions exhibit many unique properties; notably, entire microbial communities often invade one another, a phenomenon known as community coalescence. In spite of the potential importance of this process for the dynamics and stability of microbiome assembly, our understanding of it is still very limited. Recent theoretical and empirical work has proposed that large microbial communities may exhibit an emergent cohesiveness, as a result of collective consumer-resource interactions and metabolic feedbacks between microbial growth and the environment. A fundamental prediction of this proposal is the presence of ecological co-selection during community coalescence, where the invasion success of a given taxon is determined by its community members. To establish the generality of this prediction in experimental microbiomes, we have performed over one hundred invasion and coalescence experiments with environmental communities of different origins that had spontaneously and stably assembled in two different synthetic aerobic environments. We show that the dominant species of the coalesced communities can both recruit their community members (top-down co-selection) and be recruited by them (bottom-up co-selection) into the coalesced communities. Our results provide direct evidence that collective invasions generically produce ecological co-selection of interacting species, emphasizing the importance of community-level interactions during microbial community assembly.

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Microbial community composition and reactor performance during hydrogen production in a UASB reactor fed with raw cheese whey inoculated with compost

Water Science & Technology ◽

10.2166/wst.2011.706 ◽

2011 ◽

Vol 64 (11) ◽

pp. 2265-2273 ◽

Cited By ~ 31

Author(s):

E. Castelló ◽

V. Perna ◽

J. Wenzel ◽

L. Borzacconi ◽

C. Etchebehere

Keyword(s):

Microbial Community ◽

Hydrogen Production ◽

Cheese Whey ◽

Microbial Community Composition ◽

Uasb Reactor ◽

Hydrogen Yield ◽

Reactor Performance ◽

Loading Rates ◽

Streptococcus A ◽

Selection Of

This study investigated the microbial community developed in a UASB reactor for hydrogen production and correlated it to reactor performance. The reactor was inoculated with kitchen waste compost and fed with raw cheese whey at two organic loading rates, 20 gCOD/Ld and 30 gCOD/Ld. Hydrogen production was very variable, using an OLR of 30 gCOD/Ld averaged 1.0 LH2/Ld with no methane produced under these conditions. The hydrogen yield was also very variable and far from the theoretical. This low yield could be explained by selection of a mixed fermentative population with presence of hydrogen producing organisms (Clostridium, Ruminococcus and Enterobacter) and other non-hydrogen producing fermenters (Lactobacillus, Dialister and Prevotella). The molecular analysis of the raw cheese whey used for feeding revealed the presence of three predominant organisms that are affiliated with the genera Buttiauxella (a low-yield hydrogen producer) and Streptococcus (a lactic acid-producing fermenter). Although these organisms did not persist in the reactor, the continuous addition of these fermenters could decrease the reactor's hydrogen yield.

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