Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production

2021 ◽  
pp. 110294
Author(s):  
Jingxia Fu ◽  
Li Chen ◽  
Shengzhi Yang ◽  
Yuzhu Li ◽  
Lei Jin ◽  
...  
Keyword(s):  
Microbial Community ◽  
Metabolic Potential ◽  
Pit Mud

Analysis of Microbial Community Structure and Volatile Compounds in the Pit Mud Used for Manufacturing Taorong-type Baijiu Based on High-Throughput Sequencing

2021 ◽  
Author(s):  
Yanbo Liu ◽  
Mengxiao Sun ◽  
Pei Hou ◽  
Wenya Wang ◽  
Xiangkun Shen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Qualitative Analysis ◽  
Volatile Compounds ◽  
High Throughput ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Solid Phase ◽  
Gas Chromatography Mass Spectrometry ◽  
Pit Mud

Abstract In this study, the pit mud used in manufacturing Taorong-type Baijiu was collected from the upper, middle, lower and bottom layers of pits in Henan Yangshao Liquor Co., LTD. Besides, high-throughput sequencing (HTS) technology was adopted to analyze the microbial community structure of the pit mud. In addition, the volatile compounds in the pit mud were subjected to preliminarily qualitative analysis through headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The results of HTS demonstrated that there were 5, 3, 5 and 5 dominant bacterial phyla (including 11, 11, 9 and 8 dominant bacterial genera) and 3, 3, 3 and 3 dominant fungal phyla (including 4, 7, 7 and 5 dominant fungal genera) in the pit mud from F-S (upper), G-Z (middle), H-X (lower) and I-D (bottom), respectively. The qualitative analysis results of volatile compounds demonstrated that a total of 78 kinds of volatile compounds were detected in the pit mud, including 46, 45, 39 and 49 kinds in the pit mud from F-S, G-Z, H-X and I-D, respectively. Ester and acid were the two main components in the pit mud. Meanwhile, the correlation between microorganisms and main volatile compounds in the pit mud was analyzed. Moreover, Lentimicrobium, Syner-01 and Blvii28_wastewater-sludge group were found for the first time in the pit mud used for manufacturing Taorong-type Baijiu. The findings of this study could provide a theoretical foundation for improving the quality of pit mud and the flavor of Taorong-type Baijiu.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals One step towards bioremediating a heavily polluted river: Metagenomic insights on the function of microbial community

2019 ◽  
Author(s):  
Luz Breton-Deval ◽  
Ayixon Sanchez-Reyes ◽  
Alejandro Sánchez-Flores ◽  
Katy Juárez ◽  
Patricia Mussali-Galante
Keyword(s):  
Microbial Community ◽  
Broad Spectrum ◽  
Water Samples ◽  
Shotgun Sequencing ◽  
Metabolic Potential ◽  
Polluted River ◽  
Future Design ◽  
Functional Potential ◽  
One Step ◽  
Bioremediation Processes

ABSTRACTThe objective of this study is to understand the functional potential of the microbial community related to bioremediation activity and its relationship with the pollution of each site to enhance the future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1-S4), and a whole metagenome shotgun sequencing was performed to know and understand the microbial community involved in bioremediation. Additionally, HMMER was used for searching sequence homologs related to PET and polystyrene biodegradation and metal transformation in Apatlaco River metagenomes. The Apatlaco River is characterized by the presence of a broad spectrum of microorganisms with the metabolic potential to carry out bioremediation activities. Every site along the Apatlaco River has a particular community to perform bioremediation activities. The first site S1 has Thiomonas, Polaromonas, Pedobacter, and Myroides, S2 has Pedobacter, Myroides, Pseudomonas and Acinetobacter, S3, Thiomonas, Myroides, Pseudomonas, Acinetobacter and Aeromonas; S4, Thiomonas, Myroides and Pseudomonas, Thauera.Furthermore, every site is rich in specific enzymes such as S1 has dioxygenase and dehydrogenase, which can degrade Catechol, Biphenyl, Naphthalene, and Phthalate. While, S2 and S3 are rich in dioxygenase and decarboxylating dehydrogenases to degrade Toluene, Fluorobenzoate, Xylene, Phenylpropanoate, and Phenol. S3 also has monooxygenases which degrade Benzene, and all the earlier mentioned enzymes were also found at S4.

scholarly journals New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh

2020 ◽  
Author(s):  
Olivia U. Mason ◽  
Patrick Chanton ◽  
Loren N. Knobbe ◽  
Julian Zaugg ◽  
Behzad Mortazavi
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Microbial Diversity ◽  
Ecosystem Functions ◽  
Juncus Roemerianus ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Marsh Vegetation ◽  
Core Microbiome ◽  
N Removal

AbstractCoastal salt marshes are some of the most productive ecosystems on Earth, providing numerous services such as soil carbon storage, flood protection and nutrient filtering, several of which are mediated by the sediment microbiome associated with marsh vegetation. Here, nutrient filtering (nitrate removal through denitrification) was examined by determining microbial community structure (16S rRNA gene iTag sequencing), diversity, denitrification rates and metabolic potential (assembled metagenomic sequences) in collocated patches of Spartina alterniflora (Spartina) and Juncus roemerianus (Juncus) sediments. The iTag data showed that diversity and richness in Spartina and Juncus sediment microbial communities were highly similar. However, microbial community evenness differed significantly, with the most even communities observed in Juncus sediments. Further, denitrification rates were significantly higher in Juncus compared to Spartina, suggesting oscillations in microbial abundances and in particular the core microbiome identified herein, along with plant diversity influence marsh nitrogen (N) removal. Amplicon and assembled metagenome sequences pointed to a potentially important, yet unappreciated Planctomycetes role in N removal in the salt marsh. Thus, perturbations, such as sea-level rise, that can alter marsh vegetation distribution could impact microbial diversity and may ultimately influence the ecologically important ecosystem functions the marsh sediment microbiome provides.

scholarly journals Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Nunzia Picone ◽  
Carmen Hogendoorn ◽  
Geert Cremers ◽  
Lianna Poghosyan ◽  
Arjan Pol ◽  
...  
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas ◽  
Relative Abundance ◽  
Hot Spots ◽  
Microbial Community Composition ◽  
Metagenomic Analysis ◽  
Volcanic Soil ◽  
Metabolic Potential ◽  
Gas Emissions ◽  
Geothermal Activity

ABSTRACT Volcanic and geothermal environments are characterized by low pH, high temperatures, and gas emissions consisting of mainly CO2 and varied CH4, H2S, and H2 contents which allow the formation of chemolithoautotrophic microbial communities. To determine the link between the emitted gases and the microbial community composition, geochemical and metagenomic analysis were performed. Soil samples of the geothermic region Favara Grande (Pantelleria, Italy) were taken at various depths (1 to 50 cm). Analysis of the gas composition revealed that CH4 and H2 have the potential to serve as the driving forces for the microbial community. Our metagenomic analysis revealed a high relative abundance of Bacteria in the top layer (1 to 10 cm), but the relative abundance of Archaea increased with depth from 32% to 70%. In particular, a putative hydrogenotrophic methanogenic archaeon, related to Methanocella conradii, appeared to have a high relative abundance (63%) in deeper layers. A variety of [NiFe]-hydrogenase genes were detected, showing that H2 was an important electron donor for microaerobic microorganisms in the upper layers. Furthermore, the bacterial population included verrucomicrobial and proteobacterial methanotrophs, the former showing an up to 7.8 times higher relative abundance. Analysis of the metabolic potential of this microbial community showed a clear capacity to oxidize CH4 aerobically, as several genes for distinct particulate methane monooxygenases and lanthanide-dependent methanol dehydrogenases (XoxF-type) were retrieved. Analysis of the CO2 fixation pathways showed the presence of the Calvin-Benson-Bassham cycle, the Wood-Ljungdahl pathway, and the (reverse) tricarboxylic acid (TCA) cycle, the latter being the most represented carbon fixation pathway. This study indicates that the methane emissions in the Favara Grande might be a combination of geothermal activity and biological processes and further provides insights into the diversity of the microbial population thriving on CH4 and H2. IMPORTANCE The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that most of the microorganisms in this extreme environment are only distantly related to cultivated bacteria. The results obtained profoundly increased the understanding of these natural hot spots of greenhouse gas production/degradation and will help to enrich and isolate the microbial key players. After isolation, it will become possible to unravel the molecular mechanisms by which they adapt to extreme (thermo/acidophilic) conditions, and this may lead to new green enzymatic catalysts and technologies for industry.

scholarly journals Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

2011 ◽  
Vol 77 (7) ◽  
pp. 2264-2274 ◽  
Author(s):  
Ji Young Jung ◽  
Se Hee Lee ◽  
Jeong Myeong Kim ◽  
Moon Su Park ◽  
Jin-Woo Bae ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Sequences ◽  
Leuconostoc Mesenteroides ◽  
16S Rrna Genes ◽  
Read Length ◽  
Rrna Genes ◽  
Genetic Profile ◽  
Average Read Length ◽  
Metabolic Potential ◽  
Fermentation Products

ABSTRACTKimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

scholarly journals Characterization of Microbial Diversity and Community Structure in Fermentation Pit Mud of Different Ages for Production of Strong-Aroma Baijiu

2020 ◽  
Vol 69 (2) ◽  
pp. 151-164
Author(s):  
XU-JIA WANG ◽  
HONG-MEI ZHU ◽  
ZHI-QIANG REN ◽  
ZHI-GUO HUANG ◽  
CHUN-HUI WEI ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Acid Production ◽  
Diversity Index ◽  
Phospholipid Fatty Acid ◽  
Caproic Acid ◽  
Study Results ◽  
Pit Mud

In the traditional fermentation process of strong-aroma Baijiu, a fermentation pit mud (FPM) provides many genera of microorganisms for fermentation. However, the functional microorganisms that have an important effect on the quality of Baijiu and their changes with the age of fermentation pit (FP) are poorly understood. Herein, the Roche 454 pyrosequencing technique and a phospholipid fatty-acid analysis were employed to reveal the structure and diversity of prokaryotic communities in FPM samples that have been aged for 5, 30, and 100 years. The results revealed an increase in total prokaryotic biomass with an FP age; however, Shannon’s diversity index decreased significantly (p < 0.01). These results suggested that a unique microbial community structure evolved with uninterrupted use of the FP. The number of functional microorganisms, which could produce the flavor compounds of strong-aroma Baijiu, increased with the FP age. Among them, Clostridium and Ruminococcaceae are microorganisms that directly produce caproic acid. The increase of their relative abundance in the FPM might have improved the quality of strong-aroma Baijiu. Syntrophomonas, Methanobacterium, and Methanocorpusculum might also be beneficial to caproic acid production. They are not directly involved but provide possible environmental factors for caproic acid production. Overall, our study results indicated that an uninterrupted use of the FP shapes the particular microbial community structure in the FPM. This research provides scientific support for the concept that the aged FP yields a high-quality Baijiu.

scholarly journals Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis

2019 ◽  
Author(s):  
Itzel Gaytán ◽  
Ayixon Sánchez-Reyes ◽  
Manuel Burelo ◽  
Martín Vargas-Suárez ◽  
Ivan Liachko ◽  
...  
Keyword(s):  
Microbial Community ◽  
Metagenomic Analysis ◽  
Contaminated Sites ◽  
Physical Analysis ◽  
Glycol Ethers ◽  
Metabolic Potential ◽  
Proximity Ligation ◽  
Polyurethane Acrylate ◽  
Biodegradation Process ◽  
Genes Encoding

ABSTRACTPolyurethanes (PU) are the sixth more produced plastics with around 19-million tons/year, but since they are not recyclable they are burned or landfilled, generating ecological damage. To elucidate the mechanisms that landfill microbial communities perform to attack recalcitrant PU plastic, we studied the BP8 community selected by its capability to grow in a water PU dispersion (WPUD) that contains a polyether-polyurethane-acrylate (PE-PU-A) copolymer and xenobiotic additives (N-methyl 2-pyrrolidone, isopropanol and glycol ethers), and performed a proximity ligation-based metagenomic analysis for revealing the community structure and potential biodegradative capacity. Additives were consumed early whereas the copolymer was cleaved throughout the 25-days incubation. BP8 metagenomic deconvolution reconstructed five genomes, three of them from novel species. Genes encoding enzymes for additives biodegradation were predicted. The chemical and physical analysis of the biodegradation process, and the identified biodegradation products show that BP8 cleaves esters, aromatic urethanes, C-C and ether groups by hydrolytic and oxidative mechanisms. The metagenomic analysis allowed to predicting comprehensive metabolic pathways and enzymes that explain the observed PU biodegradation. This is the first study revealing the metabolic potential of a landfill microbial community that thrives within a WPUD system and shows potential for bioremediation of polyurethane- and xenobiotic additives-contaminated sites.

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