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1. An Ecosystems Perspective on Virus Evolution and Emergence

Author:
French, Rebecca K.; Holmes, Edward C.
Source:
Trends in microbiology 2020 v.28 no.3 pp. 165-175
ISSN:
0966-842X
Subject:
metagenomics,   etc   ; ecosystems; environmental health; evolution; pathogens;     Show all 5 Subjects
Abstract:
... Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host individuals, populations ...
DOI:
10.1016/j.tim.2019.10.010

2. Structural and functional insights about unique extremophilic bacterial lipolytic enzyme from metagenome source

Author:
Kaur, Ramanpreet; Kumar, Rajender; Verma, Swati; Kumar, Arbind; Rajesh, C.; Sharma, Pushpender Kumar
Source:
International journal of biological macromolecules 2020 v.152 pp. 593-604
ISSN:
0141-8130
Subject:
metagenomics,   etc   ; active sites; binding sites; calcium; enzyme activity; molecular dynamics;     Show all 6 Subjects
Abstract:
... In the present investigation, a lipid hydrolyzing gene RPK01 was cloned from metagenome source of hot spring. Expression and purification of recombinant protein revealed single purified protein band of ~24 KDa on 12% SDS-PAGE, and is well corroborated with the deduced molecular weight of protein as calculated from its amino acid sequence. The purified protein displayed high activity towards short ...
DOI:
10.1016/j.ijbiomac.2020.02.210

3. Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis?

Author:
Almeida, Janaina Marques; Alnoch, Robson Carlos; Souza, Emanuel Maltempi; Mitchell, David Alexander; Krieger, Nadia
Source:
Biochimica et biophysica acta 2020 v.1868 no.2 pp. 140320
ISSN:
1570-9639
Subject:
metagenomics,   etc   ; biocatalysis; carboxylic ester hydrolases; genomic libraries; microbial communities;     Show all 5 Subjects
Abstract:
... In recent years, metagenomic strategies have been widely used to isolate and identify new enzymes from uncultivable components of microbial communities. Among these enzymes, various lipases have been obtained from metagenomic libraries from different environments and characterized. Although many of these lipases have characteristics that could make them interesting for application in biocatalysis, ...
DOI:
10.1016/j.bbapap.2019.140320

4. Bacterial community structure and gene function prediction in response to long-term running of dual graphene modified bioelectrode bioelectrochemical systems

Author:
Chen, Junfeng; Liu, Yanyan; Yang, Yuewei; Tang, Meizhen; Wang, Renjun; Jiang, Liting; Tian, Yuping; Hu, Hanwen; Zhang, Xiao; Wei, Yushan
Source:
Bioresource technology 2020 v.309 pp. 123398
ISSN:
0960-8524
Subject:
metagenomics,   etc   ; Chthonomonas; Clostridium; Proteobacteria; bacteria; bacterial communities; bioanodes; biocathodes; bioelectrochemistry; community structure; energy metabolism; graphene; prediction;     Show all 13 Subjects
Abstract:
... This work studied bacterial community structure and gene function prediction in long-term running of dual graphene modified bioelectrode bioelectrochemical systems (LT D-GM-BE BES, 2 year). The maximum power density of LT D-GM-BE BES was 99.03 ± 3.64 mW/m², which was 3.66 times of dual control BES (D-C-BE BES), and the transfer resistance of LT GM-BE was just approximately 1/4 of control bioelectr ...
DOI:
10.1016/j.biortech.2020.123398

5. Bioremediation of intertidal zones polluted by heavy oil spilling using immobilized laccase-bacteria consortium

Author:
Dai, Xiaoli; Lv, Jing; Yan, Guangxu; Chen, Chunmao; Guo, Shaohui; Fu, Pengcheng
Source:
Bioresource technology 2020 v.309 pp. 123305
ISSN:
0960-8524
Subject:
metagenomics,   etc   ; alkanes; bacteria; biodiversity; bioremediation; coasts; littoral zone; oils; pollutants; pollution; polycyclic aromatic hydrocarbons; spectrometers;     Show all 12 Subjects
Abstract:
... Heavy oil pollution in the intertidal zones has become a worldwide environmental problem. In this study, bioremediation on heavy oil pollutants in the intertidal zones using an immobilized laccase-bacteria consortium system was evaluated with the aid of intertidal experimental pools built in the coastal area. It is found that degradation efficiency of the immobilized laccase-bacteria consortium fo ...
DOI:
10.1016/j.biortech.2020.123305

6. Investigating the mycobiome of the Holcomb Creosote Superfund Site

Author:
Czaplicki, Lauren M.; Redfern, Lauren K.; Cooper, Ellen M.; Ferguson, P. Lee; Vilgalys, Rytas; Gunsch, Claudia K.
Source:
Chemosphere 2020 v.252 pp. 126208
ISSN:
0045-6535
Subject:
metagenomics,   etc   ; Ascomycota; bioavailability; bioremediation; creosote; extracellular enzymes; fungal communities; fungi; genes; hydrophobicity; microbiome; polycyclic aromatic hydrocarbons;     Show all 12 Subjects
Abstract:
... Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were ...
DOI:
10.1016/j.chemosphere.2020.126208

7. The mechanism of nitrate-Cr(VI) reduction mediated by microbial under different initial pHs

Author:
Hu, Yutian; Chen, Nan; Liu, Tong; Feng, Chuanping; Ma, Linlin; Chen, Si; Li, Miao
Source:
Journal of hazardous materials 2020 v.393 pp. 122434
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; aquifers; bacteria; biochemical pathways; bioremediation; chromium; energy; gene expression regulation; genes; nitrates; pH;     Show all 11 Subjects
Abstract:
... To date, comparatively little research is known about the role of pH conditions in bioremediation of Cr(VI) contaminated aquifers. This study explored microbial Cr(VI) reduction and denitrification under different initial pHs. The underlying mechanism was also investigated. When testing 50 mg/L–N nitrate and 10 mg/L Cr(VI), complete contaminants removal was observed at initial pH 10.0 and 11.0, and ...
DOI:
10.1016/j.jhazmat.2020.122434

8. A novel strategy for anammox consortia preservation: Transformation into anoxic sulfide oxidation consortia

Author:
Shi, Zhi-Jian; Xu, Lian-Zeng-Ji; Huang, Bao-Cheng; Jin, Ren-Cun
Source:
The Science of the total environment 2020 v.723 pp. 138094
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; anaerobic ammonium oxidation; biochemical pathways; biomass; bioreactors; microorganisms; nitrates; nitrogen; oxidation; polymers; sludge; sulfides;     Show all 12 Subjects
Abstract:
... The preservation of anaerobic ammonia oxidation (anammox) consortia is crucial for the rapid start-up and the process stability of the anammox based bioreactor. This work proposed and evaluated the feasibility of an anammox consortia preservation strategy, in which the anammox sludge was transformed into intermediate anoxic sulfide oxidation (ASO) functional microorganisms. Initially, the ASO proc ...
DOI:
10.1016/j.scitotenv.2020.138094

9. Changed bacterial community in the river water samples upon introduction of biodegradable poly(3-hydroxybutyrate)

Author:
Kadoya, Ryosuke; Tanaka, Naoto; Fujita, Nobuyuki; Shiwa, Yuh; Taguchi, Seiichi
Source:
Polymer degradation and stability 2020 v.176 pp. 109144
ISSN:
0141-3910
Subject:
metagenomics,   etc   ; bacteria; bacterial communities; biodegradability; biodegradation; biodiversity; poly-3-hydroxybutyrate; polyethylene; river water; rivers; statistical analysis;     Show all 11 Subjects
Abstract:
... The addition effects of polymeric materials on natural environments have been mainly evaluated in terms of the relationships between culturable polymer-degrading microorganisms and/or their secreted enzymes and target materials. In this study, we applied metagenome analysis to better understand the change in unculturable microorganismal biodiversity in the four different river samples by using pol ...
DOI:
10.1016/j.polymdegradstab.2020.109144

10. The metagenome-assembled genome of Candidatus Oenococcus aquikefiri from water kefir represents the species Oenococcus sicerae

Author:
Verce, Marko; De Vuyst, Luc; Weckx, Stefan
Source:
Food microbiology 2020 v.88 pp. 103402
ISSN:
0740-0020
Subject:
metagenomics,   etc   ; Oenococcus; ciders; citrates; ecosystems; fermentation; kefir; nucleotide sequences; operon; ribosomal RNA; transferases;     Show all 11 Subjects
Abstract:
... Recently, a metagenomic study of a water kefir fermentation ecosystem enabled the reconstruction of a metagenome-assembled genome (MAG) of an Oenococcus species that was different from the three species of this genus known so far. Therefore, the name Candidatus Oenococcus aquikefiri was proposed for this novel Oenococcus species. In the meantime, however, a fourth member of the genus, Oenococcus s ...
DOI:
10.1016/j.fm.2019.103402

11. Metagenomic insights into virus removal performance of an algal-based wastewater treatment system utilizing Galdieria sulphuraria

Author:
Delanka-Pedige, Himali M.K.; Cheng, Xiaoxiao; Munasinghe-Arachchige, Srimali P.; Abeysiriwardana-Arachchige, Isuru S.A.; Xu, Jiannong; Nirmalakhandan, Nagamany; Zhang, Yanyan
Source:
Algal research 2020 v.47 pp. 101865
ISSN:
2211-9264
Subject:
metagenomics,   etc   ; Enterovirus; Norovirus; algae; animal pathogens; chlorination; coliphages; nutrients; quantitative analysis; virulent strains; wastewater treatment;     Show all 11 Subjects
Abstract:
... An algal wastewater treatment system capable of reducing dissolved organics, nutrients, and pathogenic bacteria to secondary discharge standards in a single step has been reported on previously. The current study evaluates pathogenic virus reduction in this algal wastewater treatment system and compares it with that in conventional wastewater treatment systems using culture- and nucleic acid-based ...
DOI:
10.1016/j.algal.2020.101865

12. Small scale fungal community differentiation in a vineyard system

Author:
Knight, Sarah J.; Karon, Ophir; Goddard, Matthew R.
Source:
Food microbiology 2020 v.87 pp. 103358
ISSN:
0740-0020
Subject:
metagenomics,   etc   ; fermentation; fruits; fungal communities; microbiome; population genetics; sensory properties; vineyards; wines; yeasts; New Zealand;     Show all 11 Subjects
Abstract:
... Microbes influence the quality of agricultural commodities and contribute to their distinctive sensorial attributes. Increasingly studies have demonstrated not only differential geographic patterns in microbial communities and populations, but that these contribute to valuable regionally distinct agricultural product identities, the most well-known example being wine. However, little is understood ...
DOI:
10.1016/j.fm.2019.103358

13. Metagenomics revealed the phase-related characteristics during rapid development of halotolerant aerobic granular sludge

Author:
Li, Wei; Yao, Jin-chi; Zhuang, Jin-long; Zhou, Yuan-yuan; Shapleigh, James P.; Liu, Yong-di
Source:
Environment international 2020 v.137 pp. 105548
ISSN:
0160-4120
Subject:
metagenomics,   etc   ; Geotrichum; activated sludge; bacterial adhesion; fungi; particle size; polymers; salinity; salt tolerance; sewage treatment; wastewater;     Show all 11 Subjects
Abstract:
... Efforts to produce aerobic granular sludge (AGS) for high-efficient and stable nutrient removal in high saline wastewaters have gained much attention recently. This study was undertaken to describe the phase-related characteristics of the rapid formation of glucose-fed salt-tolerant AGS (SAGS) generated from common municipal activated sludge using metagenomic approaches. The time needed for SAGS f ...
DOI:
10.1016/j.envint.2020.105548

14. Zearalenone-induced aberration in the composition of the gut microbiome and function impacts the ovary reserve

Author:
Tan, Shaojing; Ge, Wei; Wang, Junjie; Liu, Wenxiang; Zhao, Yong; Shen, Wei; Li, Lan
Source:
Chemosphere 2020 v.244 pp. 125493
ISSN:
0045-6535
Subject:
metagenomics,   etc   ; Lachnospiraceae; diet; dose response; intestinal microorganisms; lysophosphatidylcholine; metabolism; metabolites; mice; reproduction; sequence analysis; toxicity; zearalenone;     Show all 13 Subjects
Abstract:
... Zearalenone (ZEA), as a contaminant commonly found in our daily diet, has been widely studied for its toxicity. However, the exact mechanism underlying ZEA induced reproduction disorders remains unclear. Our study aimed to elucidate the underlying relationship between aberrations in the gut microbiota and the degeneration of the ovarian reserve following exposure to ZEA. Four-week-old mice were tr ...
DOI:
10.1016/j.chemosphere.2019.125493

15. Genome Resource for the Huanglongbing Causal Agent ‘Candidatus Liberibacter asiaticus’ Strain AHCA17 from Citrus Root Tissue in California, USA

Author:
Cai, Weili; Nunziata, Schyler; Costanzo, Stefano; Kumagai, Lucita; Rascoe, John; Stulberg, Michael J.
Source:
Plant disease 2020 v.104 no.3 pp. 627-629
ISSN:
0191-2917
Subject:
metagenomics,   etc   ; Candidatus Liberibacter asiaticus; Citrus; epidemiology; genes; greening disease; open reading frames; pathogens; pummelos; trees; California;     Show all 11 Subjects
Abstract:
... ‘Candidatus Liberibacter asiaticus’ is the unculturable causative agent of citrus huanglongbing disease. Here, we report the first citrus root metagenome sequence containing the draft genome of ‘Ca. L. asiaticus’ strain AHCA17, obtained from a pummelo tree in California. The assembled genome was 1.2 Mbp and resulted in 37 contigs (N₅₀ = 158.7 kbp) containing 1,057 predicted open reading frames and ...
DOI:
10.1094/PDIS-08-19-1735-A

16. The era of ‘omics’ technologies in the study of microbiologically influenced corrosion

Author:
Procópio, Luciano
Source:
Biotechnology letters 2020 v.42 no.3 pp. 341-356
ISSN:
0141-5492
Subject:
metagenomics,   etc   ; Archaea; Bacteroidetes; Firmicutes; Proteobacteria; alloys; bacteria; biofilm; corrosion; high-throughput nucleotide sequencing; metabolomics; methanogens;     Show all 12 Subjects
Abstract:
... Efforts to elucidate the relationships between microorganisms and metal corrosion were mainly directed to understanding the formation of biofilm structures grown on corroded surfaces. The emergence of high throughput DNA sequencing techniques has helped in the description of microbial species involved directly and indirectly in the corrosion processes of alloys. Coupled with sequencing from enviro ...
DOI:
10.1007/s10529-019-02789-w

17. Bioinformatic strategies to address limitations of 16rRNA short-read amplicons from different sequencing platforms

Author:
Bailén, María; Bressa, Carlo; Larrosa, Mar; González-Soltero, Rocío
Source:
Journal of microbiological methods 2020 v.169 pp. 105811
ISSN:
0167-7012
Subject:
metagenomics,   etc   ; Bacteroides; bacterial communities; bioinformatics; genes; pipelines; ribosomal RNA; sequence analysis;     Show all 8 Subjects
Abstract:
... Sequencing the 16S gene rRNA has become a popular method when identifying bacterial communities. However, recent studies address differences in the characterization based on sample preparation, sequencing platforms, and data analysis. In this work, we tested some of the available user-friendly protocols for data analysis with the reads obtained from the sequencing machines Illumina MiSeq and Ion T ...
DOI:
10.1016/j.mimet.2019.105811

18. Enhanced anaerobic fermentation of dairy manure by microelectrolysis in electric and magnetic fields

Author:
Qu, Guangfei; Lv, Pei; Cai, Yingying; Tu, Can; Ma, Xi; Ning, Ping
Source:
Renewable energy 2020 v.146 pp. 2758-2765
ISSN:
0960-1481
Subject:
metagenomics,   etc   ; biogas; cellulose; dairy manure; electric potential difference; fermentation; lignin; lignocellulose; magnetic fields; methane; microorganisms; pollution;     Show all 12 Subjects
Abstract:
... The degradation rate of lignocellulose and methane (CH4) content must be improved through anaerobic fermentation process engineering in order to promote the proper operation of anaerobic organic waste removal without secondary pollution and low cost. The present study investigates mesophilic anaerobic fermentation of dairy manure (DM) under weak magnetic and low operation voltage (0.3–0.8 V). The ...
DOI:
10.1016/j.renene.2019.06.050

19. Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles

Author:
Dugat-Bony, Eric; Lossouarn, Julien; De Paepe, Marianne; Sarthou, Anne-Sophie; Fedala, Yasmina; Petit, Marie-Agnès; Chaillou, Stéphane
Source:
Food microbiology 2020 v.85 pp. 103278
ISSN:
0740-0020
Subject:
metagenomics,   etc   ; DNA; cheeses; chloroform; comparative study; ecosystems; feces; fermented foods; filtration; microbial communities; phages; ultracentrifugation; virion;     Show all 13 Subjects
Abstract:
... The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environm ...
DOI:
10.1016/j.fm.2019.103278

20. Co-metabolic degradation of refractory dye: A metagenomic and metaproteomic study

Author:
Zhang, Qingyun; Xie, Xuehui; Liu, Yanbiao; Zheng, Xiulin; Wang, Yiqin; Cong, Junhao; Yu, Chengzhi; Liu, Na; Sand, Wolfgang; Liu, Jianshe
Source:
Environmental pollution 2020 v.256 pp. 113456
ISSN:
0269-7491
Subject:
metagenomics,   etc   ; bacteria; decolorization; dominant species; dyes; flora; fructose; pollutants; proteins; proteomics; secretion; yeast extract;     Show all 12 Subjects
Abstract:
... Fructose was utilized as an additional co-substrate to systematically investigate the molecular mechanism of its boosting effect for the degradation of refractory dye reactive black 5 (RB5) by a natural bacterial flora DDMZ1. A decolorizing rate of 98% was measured for sample YE + FRU(200) (with 3 g/L fructose additionally to yeast extract medium, 10% (v/v) inoculation size of flora DDMZ1, 200 mg/ ...
DOI:
10.1016/j.envpol.2019.113456