Metagenomics Study To Compare The Taxonomy And Metabolism of a Lignocellulolytic Microbial Consortium Cultured in Different Carbon Conditions

2021 ◽  
Author(s):  
Qinggeer BORJIGIN ◽  
Bizhou ZHANG ◽  
Xiaofang Yu ◽  
Julin Gao ◽  
Xin ZHANG ◽  
...  
Keyword(s):  
Microbial Consortium ◽  
Agricultural Waste ◽  
Taxonomic Diversity ◽  
Taxonomic Composition ◽  
Microbial Consortia ◽  
Rich Diversity ◽  
Cazy Database ◽  
Taxonomic Affiliation ◽  
In Situ Biodegradation

Abstract A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper).Analyses of the metagenomics taxonomic affiliation data showed considerable differences in the taxonomic composition and functional profile of the microbial consortia CS and FP. The microbial consortia CS primarily contained members from the genera Pseudomonas, Stenotrophomonas, Achromobacter, Dysgonomonas, Flavobacterium and Sphingobacterium, as well as Cellvibrio, Azospirillum, Pseudomonas, Dysgonomonas and Cellulomonas in FP. The COG and KEGG annotation analyses revealed considerable levels of diversity. Further analysis determined that the CS consortium had an increase in the acid and ester metabolism pathways, while carbohydrate metabolism was enriched in the FP consortium. Furthermore, a comparison against the CAZy database showed that the microbial consortia CS and FP contain a rich diversity of lignocellulose degrading families, in which GH5, GH6, GH9, GH10, GH11, GH26, GH42, and GH43 were enriched in the FP consortium, and GH44, GH28, GH2, and GH29 increased in the CS consortium. The degradative mechanism of lignocellulose metabolism by the two microbial consortia is similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. The lignocellulolytic microbial consortia cultured under different carbon conditions (CS and FP) differed substantially in their composition of the microbial community at the genus level. The changes in functional diversity were accompanied with variation in the composition of microorganisms, many of which are related to the degradation of lignocellulolytic materials. The genera Pseudomonas, Dysgonomonas and Sphingobacterium in CS and the genera Cellvibrio and Pseudomonas in FP exhibited a much wider distribution of lignocellulose degradative ability.

scholarly journals Abundance and Taxonomic Diversity of Bacteria Inhabiting the Sediment-Water Interface in a Marine Harbor Channel

2019 ◽  
Vol 54 (3) ◽  
pp. 407-418
Author(s):  
Piotr Perliński ◽  
Zbigniew J. Mudryk ◽  
Marta Zdanowicz
Keyword(s):  
Seasonal Fluctuation ◽  
Taxonomic Diversity ◽  
Taxonomic Composition ◽  
Bacterial Number ◽  
Water Interface ◽  
Phylogenetic Groups ◽  
Cell Counts ◽  
Study Sites ◽  
Taxonomic Groups

Abstract The abundance of bacteria inhabiting the sediment-water interface and their taxonomic composition were determined with the fluorescence in situ hybridization (FISH) method in a marine harbor channel in Ustka. Among bacteria inhabiting the studied layer Gammaproteobacteria (1.4 cells 108·dm−3) and Cytophaga-Flavobacterium (1.1 cells 108·dm−3) dominated. Vibrio and Pseudomonas represented only a small fraction of the total cell counts. All taxonomic groups of studied bacteria show significant positive correlation between their abundance. The total bacterial number varied from 3.3 to 23.5 cells 108·dm−3 and their biomass oscillated from 39.4 to 282.4 μg C·dm−3. This parameter differed along horizontal profiles, while there were no significant differences in the abundance of the studied taxonomic groups among the study sites of the channel in Ustka. The total number of bacteria as well as the abundance of bacterial phylogenetic groups were subject to seasonal fluctuation in the studied water basin.

scholarly journals Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wenjun Li ◽  
Xiaofang Li
Keyword(s):  
Community Structure ◽  
Mine Tailings ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Metal Release ◽  
Community Members ◽  
Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

scholarly journals Lifestyle of sponge symbiont phages by host prediction and correlative microscopy

2021 ◽  
Author(s):  
M. T. Jahn ◽  
T. Lachnit ◽  
S. M. Markert ◽  
C. Stigloher ◽  
L. Pita ◽  
...  
Keyword(s):  
Distinct Pattern ◽  
Microbial Consortia ◽  
Bacterial Symbionts ◽  
Correlative Microscopy ◽  
Phage Ecology ◽  
Infection Dynamics ◽  
Imaging Approach ◽  
Animal Hosts ◽  
Viral Distribution

AbstractBacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach (‘PhageFISH-CLEM‘) localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.

Novel environment friendly olive pomace-cyclohexanone formaldehyde composite resin

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Selda Sert ◽  
Nilgün Kızılcan
Keyword(s):  
Organic Solvents ◽  
Condensation Reaction ◽  
Agricultural Waste ◽  
Composite Resins ◽  
Formaldehyde Resin ◽  
Olive Pomace ◽  
Adhesion Properties ◽  
Content Type ◽  
Naoh Solution

Purpose Cyclohexanone-formaldehyde resin (CFR) was in situ modified with olive pomace (OP) in the presence of sodium hydroxide. The purpose of this study is to produce eco-friendly OP modified cyclohexanone composite resins (OPCFCR) with a one-step method that has higher condensation reaction temperature than CFR. The water absorption properties, gloss value and cross-cut adhesion properties of the product were investigated. Design/methodology/approach Cyclohexanone, formalin (37% aqueous solution) and tannin were mixed and 20% aqueous NaOH solution was added to produce the resin. OP has environmentally friendly bio-based lignin, cellulose and phenolic compounds and the OP structure has been incorporated into the structure of the CFR resin during the in situ modification, such as resole resin and polysaccharide. The weights of pomace were used as 5% and 10% of the weight of cyclohexanone in cyclohexanone-formaldehyde composite resins, respectively. Findings There is an improvement in the properties of the OPCFCR produced from an agricultural waste that is very abundant in Gulf of Edremit region of Balikesir. The OPCFCRs were soluble in common organic solvents. The product OPCFCR has a dark red-brown color. Research limitations/implications The reaction mixture must be stirred continuously. Subsequently, 37% formalin was added dropwise in total while refluxing. The amount of aqueous NaOH solution is limited as the formed resin may become insoluble in common organic solvents. At the end of the reaction, a water-insoluble resin is obtained. Practical implications This study provides the application of ketonic resins. The OPCFCR containing phenolic groups may also promote the adhesive strength of a coating. Social implications These resins may be used for the preparation of adhesive. OP, with a large amount of catechol groups, was considered for reducing the formaldehyde emission level on the adhesive system. Originality/value OPCFCR has been synthesized in the presence of a base catalyst. Environmental and ecological concerns have increased the attention paid by chemical industry to renewable raw materials.

scholarly journals In situ biodegradation, photooxidation and dissolution of petroleum compounds in Arctic seawater and sea ice

2019 ◽  
Vol 148 ◽  
pp. 459-468 ◽  
Author(s):  
Leendert Vergeynst ◽  
Jan H. Christensen ◽  
Kasper Urup Kjeldsen ◽  
Lorenz Meire ◽  
Wieter Boone ◽  
...  
Keyword(s):  
Sea Ice ◽  
In Situ Biodegradation

Antarctic notothenioid fishes as subjects for research in evolutionary biology

2000 ◽  
Vol 12 (3) ◽  
pp. 276-287 ◽  
Author(s):  
Joseph T. Eastman
Keyword(s):  
Evolutionary Biology ◽  
Fish Fauna ◽  
Taxonomic Diversity ◽  
Late Eocene ◽  
Taxonomic Composition ◽  
Species Flock ◽  
Subzero Temperatures ◽  
Key Innovation ◽  
The Antarctic ◽  
Upper Slope

Antarctica is a continental island and the waters of its shelf and upper slope are an insular evolutionary site. The shelf waters resemble a closed basin in the Southern Ocean, separated from other continents by distance, current patterns and subzero temperatures. The benthic fish fauna of the shelf and upper slope of the Antarctic Region includes 213 species with higher taxonomic diversity confined to 18 families. Ninety-six notothenioids, 67 liparids and 23 zoarcids comprise 45%, 32% and 11% of the fauna, a combined total of 88%. In high latitude (71–78°S) shelf areas notothenioids dominate abundance and biomass at levels of 90–95%. Notothenioids are also morphologically and ecologically diverse. Although they lack a swim bladder, the hallmark of the notothenioid radiation has been repeated diversification into water column habitats. There are pelagic, semipelagic, cryopelagic and epibenthic species. Notothenioids exhibit the disproportionate speciosity and high endemism characteristic of fish species flock. Antifreeze glycopeptides originating from a transformed trypsinogen gene are a key innovation. It is not known when the modern Antarctic shelf fauna assumed its current taxonomic composition. A late Eocene fossil fauna was taxonomically diverse and cosmopolitan. There was a subsequent faunal replacement with little carryover of families into the modern fauna. Basal notothenioid clades probably diverged in Gondwanan shelf locations during the early Tertiary. Dates inferred from molecular sequences suggest that phyletically derived Antarctic clades arose 15–5 m.y.a.

scholarly journals How Early Diagenesis Reveals in Situ Biodegradation of Herbicides in Sediment

10.5772/13298 ◽  
2011 ◽  
Author(s):  
Devault Damien ◽  
Delmotte Sbastien ◽  
Macarie Herv ◽  
Dolfing Jan ◽  
Anschutz Pierre
Keyword(s):  
Early Diagenesis ◽  
In Situ Biodegradation

scholarly journals Current Advances in the Biodegradation and Bioconversion of Polyethylene Terephthalate

2021 ◽  
Vol 10 (1) ◽  
pp. 39
Author(s):  
Xinhua Qi ◽  
Wenlong Yan ◽  
Zhibei Cao ◽  
Mingzhu Ding ◽  
Yingjin Yuan
Keyword(s):  
Polyethylene Terephthalate ◽  
Microbial Consortium ◽  
Tricarboxylic Acid Cycle ◽  
Tca Cycle ◽  
Tricarboxylic Acid ◽  
Microbial Consortia ◽  
Plastic Pollution ◽  
One Step ◽  
Complex Polymers ◽  
The One

Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and modified, which mainly act on and degrade the ester bond of PET. The monomers, TPA and EG, can be further utilized by microorganisms, entering the tricarboxylic acid cycle (TCA cycle) or being converted into high value chemicals, and finally realizing the biodegradation and bioconversion of PET. Based on synthetic biology and metabolic engineering strategies, this review summarizes the current advances in the modified PET hydrolases, engineered microbial chassis in degrading PET, bioconversion pathways of PET monomers, and artificial microbial consortia in PET biodegradation and bioconversion. Artificial microbial consortium provides novel ideas for the biodegradation and bioconversion of PET or other complex polymers. It is helpful to realize the one-step bioconversion of PET into high value chemicals.

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