Primer sequences for 16S or 18S rRNA sequencing.
\r\n\t
",isbn:"978-1-83881-017-7",printIsbn:"978-1-83881-016-0",pdfIsbn:"978-1-83881-024-5",doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,hash:"d5ac3a7054e526666a89271cef6ee869",bookSignature:"Dr. Ahmed Mourtada Elseman",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/9924.jpg",keywords:"Photons, Semiconducting Materials, Photocurrent Density, Dye-Sensitized Cells, Perovskite Cells, Perovskite/Si Tandem, CIGS, CdTe, Single Crystal, Thin-Film Crystal, Single Crystal, Multicrystalline",numberOfDownloads:820,numberOfWosCitations:0,numberOfCrossrefCitations:0,numberOfDimensionsCitations:0,numberOfTotalCitations:0,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"May 25th 2020",dateEndSecondStepPublish:"June 15th 2020",dateEndThirdStepPublish:"August 14th 2020",dateEndFourthStepPublish:"November 2nd 2020",dateEndFifthStepPublish:"January 1st 2021",remainingDaysToSecondStep:"10 months",secondStepPassed:!0,currentStepOfPublishingProcess:5,editedByType:null,kuFlag:!1,biosketch:"Dr. Elseman holds two diplomas, first one from Inner Mongolia Institute of Science and Technology and the second one from the Institute of New Energy, Wuhan. During his work at Southwest University, where he is currently also active, Dr. Elseman received funds from Central Universities for a project on efficient perovskite solar cells, a topic on which his research is mainly focused.",coeditorOneBiosketch:null,coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"221890",title:"Dr.",name:"Ahmed Mourtada",middleName:null,surname:"Elseman",slug:"ahmed-mourtada-elseman",fullName:"Ahmed Mourtada Elseman",profilePictureURL:"https://mts.intechopen.com/storage/users/221890/images/system/221890.jpg",biography:"Ahmed Mourtada Elseman obtained his B.Sc., M.Sc., and Ph.D. in Inorganic and Analytical Chemistry from the Faculty of Science, Al-Azhar University, Egypt. He earned his Ph.D. in perovskite solar cells in February 2017. He obtained two diplomas, first one from Inner Mongolia Institute of Science and Technology, Hohhot, China 2015, and the second one from the Institute of New Energy, Wuhan, China, 2017. He currently works as Research Assistant Professor at the Department of Electronic and Magnetic Materials, Central Metallurgical Research and Development Institute (CMRDI), Egypt. \nHe was awarded the Talent Young Scientific (TYSP) Postdoctoral Research Fellow position funded by the Chinese Ministry of Science and Technology (MOST) and organized by North China Electric Power University, Beijing, China, 2017-2018. After that, he received a lecturer position in the School of Materials and Energy, Southwest University, Chongqing. China (2018 – 2020). During his work at Southwest University, he received a project funded by Central Universities for efficient perovskite solar cells (ID: XDJK2019C005). He was also awarded the CMRDI prize for excellence scientific publication (2018). His current research focuses on understanding the mechanisms, fundamental properties, and developing scalable protocols for high-efficiency perovskite solar cells. He is a reviewer and a member of the editorial board for certain international journals.",institutionString:"Central Metallurgical Research and Development Institute",position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"3",totalChapterViews:"0",totalEditedBooks:"0",institution:{name:"Central Metallurgical Research and Development Institute",institutionURL:null,country:{name:"Egypt"}}}],coeditorOne:null,coeditorTwo:null,coeditorThree:null,coeditorFour:null,coeditorFive:null,topics:[{id:"11",title:"Engineering",slug:"engineering"}],chapters:[{id:"76186",title:"Effect of Combination of Natural Dyes and the Blocking Layer on the Performance of DSSC",slug:"effect-of-combination-of-natural-dyes-and-the-blocking-layer-on-the-performance-of-dssc",totalDownloads:3,totalCrossrefCites:0,authors:[null]},{id:"75064",title:"A New Generation of Energy Harvesting Devices",slug:"a-new-generation-of-energy-harvesting-devices",totalDownloads:42,totalCrossrefCites:0,authors:[null]},{id:"73305",title:"Thin-Film Solar Cells Performances Optimization: Case of Cu (In, Ga) Se2-ZnS",slug:"thin-film-solar-cells-performances-optimization-case-of-cu-in-ga-se2-zns",totalDownloads:45,totalCrossrefCites:0,authors:[null]},{id:"74344",title:"Solar Energy Assessment in Various Regions of Indian Sub-continent",slug:"solar-energy-assessment-in-various-regions-of-indian-sub-continent",totalDownloads:71,totalCrossrefCites:0,authors:[null]},{id:"75972",title:"Modeling of Photovoltaic Module",slug:"modeling-of-photovoltaic-module",totalDownloads:13,totalCrossrefCites:0,authors:[null]},{id:"73549",title:"Nanostructured Transition Metal Compounds as Highly Efficient Electrocatalysts for Dye-Sensitized Solar Cells",slug:"nanostructured-transition-metal-compounds-as-highly-efficient-electrocatalysts-for-dye-sensitized-so",totalDownloads:67,totalCrossrefCites:0,authors:[{id:"30213",title:"Dr.",name:"Chuan-Pei",surname:"Lee",slug:"chuan-pei-lee",fullName:"Chuan-Pei Lee"},{id:"281675",title:"Dr.",name:"Yi-June",surname:"Huang",slug:"yi-june-huang",fullName:"Yi-June Huang"}]},{id:"74431",title:"IIIrd Generation Solar Cell",slug:"iiird-generation-solar-cell",totalDownloads:1,totalCrossrefCites:0,authors:[null]},{id:"73730",title:"Graphene-Based Material for Fabrication of Electrodes in Dye-Sensitized Solar Cells",slug:"graphene-based-material-for-fabrication-of-electrodes-in-dye-sensitized-solar-cells",totalDownloads:95,totalCrossrefCites:0,authors:[null]},{id:"73328",title:"Optical Study of Porous Silicon Layers Produced Electrochemically for Photovoltaic Application",slug:"optical-study-of-porous-silicon-layers-produced-electrochemically-for-photovoltaic-application",totalDownloads:130,totalCrossrefCites:0,authors:[null]},{id:"73799",title:"2D Organic-Inorganic Hybrid Perovskite Light-Absorbing Layer in Solar Cells",slug:"2d-organic-inorganic-hybrid-perovskite-light-absorbing-layer-in-solar-cells",totalDownloads:129,totalCrossrefCites:0,authors:[null]},{id:"73569",title:"Excited-State Dynamics of Organic Dyes in Solar Cells",slug:"excited-state-dynamics-of-organic-dyes-in-solar-cells",totalDownloads:104,totalCrossrefCites:0,authors:[null]},{id:"75949",title:"Ultrasonic Processing of Si and SiGe for Photovoltaic Applications",slug:"ultrasonic-processing-of-si-and-sige-for-photovoltaic-applications",totalDownloads:12,totalCrossrefCites:0,authors:[null]},{id:"74171",title:"Study of a New Hybrid Optimization-Based Method for Obtaining Parameter Values of Solar Cells",slug:"study-of-a-new-hybrid-optimization-based-method-for-obtaining-parameter-values-of-solar-cells",totalDownloads:66,totalCrossrefCites:0,authors:[null]},{id:"74095",title:"Advanced Laser Processing Towards Solar Cells Fabrication",slug:"advanced-laser-processing-towards-solar-cells-fabrication",totalDownloads:48,totalCrossrefCites:0,authors:[null]}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"},personalPublishingAssistant:{id:"252211",firstName:"Sara",lastName:"Debeuc",middleName:null,title:"Ms.",imageUrl:"https://mts.intechopen.com/storage/users/252211/images/7239_n.png",email:"sara.d@intechopen.com",biography:"As an Author Service Manager my responsibilities include monitoring and facilitating all publishing activities for authors and editors. From chapter submission and review, to approval and revision, copyediting and design, until final publication, I work closely with authors and editors to ensure a simple and easy publishing process. I maintain constant and effective communication with authors, editors and reviewers, which allows for a level of personal support that enables contributors to fully commit and concentrate on the chapters they are writing, editing, or reviewing. I assist authors in the preparation of their full chapter submissions and track important deadlines and ensure they are met. I help to coordinate internal processes such as linguistic review, and monitor the technical aspects of the process. As an ASM I am also involved in the acquisition of editors. 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Venkateswarlu",coverURL:"https://cdn.intechopen.com/books/images_new/371.jpg",editedByType:"Edited by",editors:[{id:"58592",title:"Dr.",name:"Arun",surname:"Shanker",slug:"arun-shanker",fullName:"Arun Shanker"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"72",title:"Ionic Liquids",subtitle:"Theory, Properties, New Approaches",isOpenForSubmission:!1,hash:"d94ffa3cfa10505e3b1d676d46fcd3f5",slug:"ionic-liquids-theory-properties-new-approaches",bookSignature:"Alexander Kokorin",coverURL:"https://cdn.intechopen.com/books/images_new/72.jpg",editedByType:"Edited by",editors:[{id:"19816",title:"Prof.",name:"Alexander",surname:"Kokorin",slug:"alexander-kokorin",fullName:"Alexander Kokorin"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"314",title:"Regenerative Medicine and Tissue Engineering",subtitle:"Cells and Biomaterials",isOpenForSubmission:!1,hash:"bb67e80e480c86bb8315458012d65686",slug:"regenerative-medicine-and-tissue-engineering-cells-and-biomaterials",bookSignature:"Daniel Eberli",coverURL:"https://cdn.intechopen.com/books/images_new/314.jpg",editedByType:"Edited by",editors:[{id:"6495",title:"Dr.",name:"Daniel",surname:"Eberli",slug:"daniel-eberli",fullName:"Daniel Eberli"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"57",title:"Physics and Applications of Graphene",subtitle:"Experiments",isOpenForSubmission:!1,hash:"0e6622a71cf4f02f45bfdd5691e1189a",slug:"physics-and-applications-of-graphene-experiments",bookSignature:"Sergey Mikhailov",coverURL:"https://cdn.intechopen.com/books/images_new/57.jpg",editedByType:"Edited by",editors:[{id:"16042",title:"Dr.",name:"Sergey",surname:"Mikhailov",slug:"sergey-mikhailov",fullName:"Sergey Mikhailov"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"1373",title:"Ionic Liquids",subtitle:"Applications and Perspectives",isOpenForSubmission:!1,hash:"5e9ae5ae9167cde4b344e499a792c41c",slug:"ionic-liquids-applications-and-perspectives",bookSignature:"Alexander Kokorin",coverURL:"https://cdn.intechopen.com/books/images_new/1373.jpg",editedByType:"Edited by",editors:[{id:"19816",title:"Prof.",name:"Alexander",surname:"Kokorin",slug:"alexander-kokorin",fullName:"Alexander Kokorin"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"2270",title:"Fourier Transform",subtitle:"Materials Analysis",isOpenForSubmission:!1,hash:"5e094b066da527193e878e160b4772af",slug:"fourier-transform-materials-analysis",bookSignature:"Salih Mohammed Salih",coverURL:"https://cdn.intechopen.com/books/images_new/2270.jpg",editedByType:"Edited by",editors:[{id:"111691",title:"Dr.Ing.",name:"Salih",surname:"Salih",slug:"salih-salih",fullName:"Salih Salih"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}},{type:"book",id:"872",title:"Organic Pollutants Ten Years After the Stockholm Convention",subtitle:"Environmental and Analytical Update",isOpenForSubmission:!1,hash:"f01dc7077e1d23f3d8f5454985cafa0a",slug:"organic-pollutants-ten-years-after-the-stockholm-convention-environmental-and-analytical-update",bookSignature:"Tomasz Puzyn and Aleksandra Mostrag-Szlichtyng",coverURL:"https://cdn.intechopen.com/books/images_new/872.jpg",editedByType:"Edited by",editors:[{id:"84887",title:"Dr.",name:"Tomasz",surname:"Puzyn",slug:"tomasz-puzyn",fullName:"Tomasz Puzyn"}],productType:{id:"1",chapterContentType:"chapter",authoredCaption:"Edited by"}}]},chapter:{item:{type:"chapter",id:"65831",title:"Microbial Community Structure and Metabolic Networks in Polar Glaciers",doi:"10.5772/intechopen.84945",slug:"microbial-community-structure-and-metabolic-networks-in-polar-glaciers",body:'\nPolar glaciers have aroused great interest over the last year, and their study has increased since they are sentinels of climate change. Although both poles are extreme environments (in terms of low temperatures, high UV radiation, lack of light in winter and permanent solar radiation in summer, scarce nutrients, etc.), Arctic and Antarctic glaciers are very different. The North Pole is an ocean surrounded by land, while the South Pole is a continent surrounded by water. This distinction confers them very unique geographical and environmental characteristics.
\nMetabolically active microbial communities have been identified in both the Arctic [1] and Antarctic glaciers (Figure 1) [2]. These microbial communities include bacteria, archaea, microeukaryotes, and viruses [3].
\nPolar maps and localization of the referenced glaciers. (1) Cascade Volcano Arc [
Arctic glaciers do not reach such distant latitudes or low temperatures as Antarctic glaciers do. These are some of the reasons why they are being extremely affected by global warming. There are glaciers around the entire Arctic Ocean, but polar glaciers in North America [4, 5], Greenland [6, 7, 8], Svalbard [9, 10], and Iceland [11, 12] (Figure 1) have been the most widely studied from a microbiological point of view. Antarctic glaciers present exceptional environmental conditions. Being in higher latitudes allows the existence of very low temperatures and high rates of solar radiation in summer. Some published reports on glacial and subglacial microbiology refer to very extreme latitudes that reach −75°S in the high Antarctic Plateau [13], −77°S in Lake Vostok [14], and −84°S in the West Antarctic ice sheet [15] (Figure 1).
\nIn the study of glacier microbiology, a variety of techniques have been traditionally used, such as microscopy techniques [16], cell cultures, and isolation of microorganisms [17]. However, the most significant advance has been achieved with the application of metagenomics. This discipline has allowed both the knowledge of the microbial communities’ structure and the comprehension of their metabolic potential.
\nGlaciers have recently been considered authentic biomes [18]. It has been observed that microbial community composition depends on the area of the glacier studied [19]. In most of them, three well-defined and interconnected ecosystems can be defined: supraglacial, englacial, and subglacial ecosystems. These ecosystems are different in their solar radiation, water content, nutrient abundance, and redox potential [20]. These factors influence in the abundance and diversity of microbial populations inhabiting glaciers (Figure 2). They also affect the type of functionality and the biogeochemical cycles in these ecosystems.
\nBacterial community structure in polar glacier ecosystems based on 16S and 18S rRNA gene sequences. Pie charts represent relative abundances of bacteria, archaea, and eukarya for three glacier ecosystems: supraglacial, englacial, and subglacial. The data are from [20, 11, 10, 4, 13, 8] for bacteria, from [
The supraglacial ecosystem is the one which has best been studied. It has been reported that the main habitats in the supraglacial ecosystem are the snowpack, cryoconite holes (vertical cylindrical melt holes in a glacier surface), supraglacial streams, and moraines [20].
\nThe sunlit and oxygenated supraglacial surface is populated by autotrophic microorganisms such as cyanobacteria, microalgae, and diatoms [21], by chemolithotrophic bacteria, which feed on inorganic sand particles, and by heterotrophic bacteria and microeukaryotes [22] (Figure 2). The main bacterial classes that have been described in this ecosystem are
Among microeukaryotes, snow is mainly populated by pigmented algae, which have been observed in Arctic and Antarctic glaciers [25]. They belong to several taxa, mainly
Fungi, especially basidiomycetous yeasts and
Archaea have also been identified in glacial snow and ice, although they have not been found in all the studies that have been carried out. They belong to Nitrososphaerales, which are known as important ammonia oxidizers [11].
\nUnder the recently fallen snow, there is a layer of hard ice. This layer arises to the surface in the episodes of melting that occur during the polar summer. The ice surface constitutes a distinct type of supraglacial microhabitat that is different from cryoconite holes. It is mainly populated by microalgae (Zygnematophyceae) and by cyanobacteria [17].
\nCryoconite holes are predominantly inhabited by cyanobacteria [27]. Filamentous cyanobacteria such as
In englacial ecosystems, live motile bacteria can reach more than 3000 m of depth. These bacteria reside in clay particles and ice channels. According to their metabolism, they can be both chemoautotrophs (i.e.,
The subglacial ecosystem is dominated by aerobic and anaerobic bacteria in basal bedrock and subglacial lakes. It does also contain diverse and metabolically active archaeal, bacterial, and fungal species [25] (Figure 2).
\nAmong bacteria, species with chemolithotrophic activity have been identified; an example is
Archaea in these anoxic environments are mainly represented by methanogenic and methanotrophic species [25]. Methanogenesis, the production of methane in an anaerobic process mediated exclusively by methanogenic archaea, is a very plausible process in the subglacial ecosystem. In glacier samples from this environment, methanogenic archaea of the euryarchaeal orders Methanosarcinales [5] and Methanomicrobiales have been detected [6].
\nEukaryotes have only been found in some of the studied subglacial environments [19]. Among them, mainly fungi have been described [26].
Living in such extreme environments implies coping with low temperatures, desiccation, low nutrients availability, and ultraviolet irradiation [30]. Over the last years, metagenomics have allowed a great understanding of metabolic potentials and biogeochemical cycles in polar glaciers through reconstruction of microbial genomes (Figure 3).
\nOverview of the metabolic potentials between dominant microorganisms in the three polar glacial ecosystems. The data are from [
Regarding the supraglacial ecosystem, metagenomic studies have demonstrated the wide diversity of functions in cryoconite holes, with a range of metabolic pathways which depend on their competence to acquire and degrade available nutrients [10]. Functional analyses highlighted the importance of stress responses and efficient carbon and nutrient recycling.
\nMetagenomic techniques have also been used to identify algal communities in the supraglacial ecosystem and their relationship with geochemical factors [12].
\nThe potential of archaea as important ammonia oxidizers has been another finding achieved by metagenomics [11].
\nLittle is known about the metabolic potential and the biogeochemical cycles of microbial communities inhabiting the englacial ecosystem. It has been reported that microorganisms enclosed in the englacial ice present very low metabolic rates, using energy only to repair damaged biomolecules and not to grow and reproduce [31].
\nIn the subglacial ecosystem, some metagenomics data implied that the most abundant and active component were bacteria within the order
At least three modes of carbon fixation were inferred [14]. The most common mode of carbon fixation was the reductive pentose phosphate cycle. The second in frequency was the reductive tricarboxylic acid pathway. This cycle also produces precursors for nucleic acid and aromatic amino acid syntheses. The third type of carbon fixation, the reductive acetyl-CoA pathway, is the one used by archaea [14].
\nThese investigations did also identify genes that carry out various parts of the nitrogen cycle, including nitrogen fixation (
Characterization of the Antarctic Blood Falls microbial assemblage revealed taxa that could participate in active sulfur cycling, including autotrophs and heterotrophs such as
The metagenome of polar microorganisms has been widely studied in recent years. Their results can provide a great amount of information about the biodiversity, survival capacity, and functioning of microbial communities in these extreme environments. In addition, information about ancient communities preserved within glacial ice through time can be obtained [33].
\nBetween 1975 and 2005, most of the DNA sequences were obtained through the application of the Sanger techniques [34], which led to the first generation of automated DNA sequencers [35] (Figure 4). For 16S or 18S rRNA sequencing, PCR amplification was carried out with specific primers (Table 1) and sequencing instruments based on capillary electrophoresis. Nowadays, Sanger sequencing achieves high read lengths of up to 1000 bp and per base and accuracies of 99.999% [36]. In the de novo metagenomics, randomly fragmented DNA was cloned into a high-copy-number plasmid and then transformed in
Typical workflow in polar glacier metagenomics researches.
\n | Specificity | \nPrimers | \nSequence (5′ to 3′) | \nProduct length (bp) | \nAuthors | \nReference | \n
---|---|---|---|---|---|---|
Sanger | \nBacteria | \n16S-F | \nAGAGTTTGATCCTGGCTCAG | \n1000 | \nLane, 1991 | \n[45] | \n
Bacteria | \n16S-R | \nCACGAGCTGACGACAGCC | \n1000 | \nLane, 1991 | \n[45] | \n|
Archaea | \n20F | \nTTCCGGTTGATCCYGCCRG | \n1372 | \nMassana et al., 1997 | \n[46] | \n|
Archaea | \nU1392R | \nACGGGCGGTGTGTRC | \n1372 | \nMassana et al., 1997 | \n[46] | \n|
Eukarya | \nEuka1F | \nCTGGTTGATCCTGCCAG | \n500 | \nLefranc et al., 2005 | \n[47] | \n|
Eukarya | \nEuk502R | \nTGATCCTTCTGCAGGTTCACCTAC | \n500 | \nAmann et al., 1990 | \n[48] | \n|
NGS | \nBacteria | \n(V3–V4) 341F | \n100 | \nHerlemann et al., 2011 | \n[49] | \n|
Bacteria | \n(V3–V4) 805R | \n100 | \nHerlemann et al., 2011 | \n[49] | \n||
Eukarya | \n(V9) 1380F | \n43 | \nAmaral-Zettler et al., 2009 | \n[50] | \n||
Eukarya | \n(V9) 1510R | \n39 | \nAmaral-Zettler et al., 2009 | \n[50] | \n
Primer sequences for 16S or 18S rRNA sequencing.
Some examples of microorganisms from polar glaciers analyzed with these technologies were Antarctic bacteria from the Dry Valleys [37] and the Arctic ice pack [38]. In general, the number of sequences identified by this technique was scarce. However, this method has the advantage of generating long reference sequences, which are very useful for studies of taxonomy and biodiversity.
\nNext-generation sequencing (NGS) technology is similar to capillary sequencing (Figure 4). The main difference is that, instead of sequencing a single DNA fragment, NGS develops this process with millions of DNA fragments.
\nThe introduction of pyrosequencing technology by 454 life sciences in 2005 began the NGS innovation. This allowed the identification of thousands of short-sequencing reads without the need for cloning. This technique was used to research the microbial life in the Dry Valleys, Antarctica [39], and Ace Lake, Antarctica [40], and in Arctic glaciers from Svalbard [10].
\nSince then, many other NGS technologies have been developed. The Illumina platform (MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq instruments) is based on sequencing by synthesis of the complementary strand and fluorescence-based detection of reversibly blocked terminator nucleotides. The platform includes multiple instruments with varying read length. For example, Illumina sequencing has been employed in a metagenomic research into diazotrophic communities across Arctic glacier forefields [41] and in the metagenomic analysis of basal ice from an Alaskan glacier [42]. Sequencing of 16S and 18S rDNA PCR amplicons is the most common approach to investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Recently this method has been improved with the use of 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes [43]. Furthermore, newer Illumina sequencers produce longer reads (e.g., the HiSeq2500 and MiSeq produce 2 × 150bp and 2 × 250bp reads, respectively, which after merging can generate reads up to, e.g., 290 and 490 bp).
\nOther metagenomic studies based on the Ion Torrent platform were also based on sequencing by synthesis, but the detection was performed using semiconductor technology. Ion Torrent technology was applied to analyze red snow microbiomes and their role in melting Arctic glaciers [12].
\nThe main drawback of the aforementioned second-generation sequencing platforms is that they generate relatively fragmented genome assemblies. In order to produce closed reference genomes, longer reads are required [36]. To meet this demand, third-generation sequencing platforms have been developed. These technologies directly target single DNA molecules without the need for PCR amplification. The PacBio RSII platform uses single-molecule real-time (SMRT) sequencing technology which allows to obtain extremely long DNA fragments of 20 kb and even longer [43].
\nEnvironmental microbiome sequencing analysis consists of binning sequencing reads into taxonomic units to compare the microbial composition of samples. This information will allow the knowledge of the microbial population taxonomy, diversity, and functioning. When these data are correlated to certain environmental parameters, both ecological and biogeochemical analysis can be performed. Taxonomic binning of 16S and 18S rRNA reads is usually based on one of these four databases: SILVA, Ribosomal Database Project, Greengenes, and NCBI [44]. For instance, the Ribosomal Database Project was used to perform a metagenomic analysis if Illumina sequences to identify bacterial communities in Antarctic surface snow [45].
\nSeveral tools have been developed to investigate the taxonomic composition of metagenomes and, in some cases, the functional composition of the community. These tools can be classified into two groups: those that use all the available sequences (MEGAN/MEGAN4, MG-RAST, Genometa, Kraken, LMAT, Taxator-tk, CLARK, GOTTCHA, EBI) and those that use a set of genes (MetaPhyler, QIIME6, mOTU, MetaPhlAn, One Codex) [33]. These genome analysis tools are summarized in Table 2.
\nCategory | \nTool\n1\n\n | \nTaxonomy\n2\n\n | \nFunction | \nURL | \n
---|---|---|---|---|
Use all available sequences | \nMEGAN/MEGAN4 | \nB | \n+ | \n\nhttps://ab.inf.uni-tuebingen.de/software/megan4\n | \n
MG-RAST | \nB/E | \n+ | \n\nhttps://www.mg-rast.org/\n | \n|
Genometa | \nB | \n− | \n\nhttp://genomics1.mh-hannover.de/genometa/\n | \n|
Kraken | \nB | \n− | \n\nhttps://ccb.jhu.edu/software/kraken/\n | \n|
LMAT | \nB | \n+ | \n\nhttps://computation.llnl.gov/projects/livermore-metagenomics-analysis-toolkit\n | \n|
Taxator-tk | \nB | \n− | \n\nhttps://github.com/fungs/taxator-tk\n | \n|
CLARK | \nB | \n− | \n\nhttp://clark.cs.ucr.edu/\n | \n|
GOTTCHA | \nB/E | \n− | \n\nhttp://lanl-bioinformatics.github.io/GOTTCHA/\n | \n|
EBI | \nB | \n+ | \n\nhttps://www.ebi.ac.uk/metagenomics/\n | \n|
Use a set of genes | \nMetaPhyler | \nB | \n− | \n\nhttp://metaphyler.cbcb.umd.edu/\n | \n
QIIME6 | \nB | \n− | \n\nhttp://qiime.org/\n | \n|
mOTU | \nB | \n− | \n\nhttps://omictools.com/motu-tool\n | \n|
MetaPhlAn | \nB/E | \n− | \n\nhttp://huttenhower.sph.harvard.edu/metaphlan2\n | \n|
One Codex | \nB/E | \n− | \n\nhttps://onecodex.com/\n | \n
Metagenome analysis tools.
Incomplete list compiled from sources.
B, bacterial taxa; E, eukaryotic taxa.
An example of the use of these tools is the metagenomics analysis with MG-RAST performed to study Arctic microbial communities [41]. Sequence analysis with QIIME was performed with cryoconite samples from Arctic glaciers [10] and with permafrost samples from the Antarctic Dry Valleys [39].
\nAlthough metagenomics is changing rapidly, still new improvements in the development of analytical tools and databases are required to answer important questions in polar glacier microbiology.
\n\n
Extraordinary advances in metagenomics have allowed a great understanding of microbial ecology and function of polar glacier microbial communities.
Important novel tools to study environmental microbiology based on metagenomics are being developed.
Third-generation technologies may further revolutionize metagenomic research.
The application of new technologies to metagenomic studies of polar glaciers will enable to link the diversity and functionality of these habitats.
Significant challenges for metagenomics remain, especially in data processing and genome analysis.
This research was supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (Grants CTM 2010-12134-E/ANT and CTM2011-16003-E) and the Institute of Health Carlos III (Grant PI14/00705). E.G.L. is a recipient of a Ciencia, Innovación y Universidades Fellowship (Grant PTA2016-12325-I, Programa Nacional de Contratación e Incorporación de RRHH). We thank Paula Alcazar for reading this manuscript and for her helpful suggestions and revisions.
\nThe authors declare that none of us has any competing commercial interests in relation to the submitted work.
Antibiotic resistance (AR) which is defined as the ability of an organism to resist the killing effects of an antibiotic to which it was normally susceptible [1] and it has become an issue of global interest [2]. This microbial resistance is not a new phenomenon since all microorganisms have an inherent capacity to resist some antibiotics [3]. However, the rapid surge in the development and spread of AR is the main cause for concern [4]. In recent years, enough evidence highlighting a link between excessive use of antimicrobial agents and antimicrobial resistance from animals as a contributing factor to the overall burden of AR has emerged [5]. The extent of usage is expected to increase markedly over coming years due to intensification of farming practices in most of the developing countries [6]. The main reasons for the use of antibiotics in food-producing animals include prevention of infections, treatment of infections, promotion of growth and improvement in production in the farm animals [7, 8].
\nPoultry is one of the most widespread food industries worldwide. Chicken is the most commonly farmed species, with over 90 billion tons of chicken meat produced per year [9]. A large diversity of antimicrobials, are used to raise poultry in most countries [10, 11, 12]. A large number of such antimicrobials are considered to be essential in human medicine [13, 14]. The indiscriminate use of such essential antimicrobials in animal production is likely to accelerate the development of AR in pathogens, as well as in commensal organisms. This would result in treatment failures, economic losses and could act as source of gene pool for transmission to humans. In addition, there are also human health concerns about the presence of antimicrobial residues in meat [15, 16], eggs [17] and other animal products [18, 19].
\nGenerally, when an antibiotic is used in any setting, it eliminates the susceptible bacterial strains leaving behind those with traits that can resist the drug. These resistant bacteria then multiply and become the dominating population and as such, are able to transfer (both horizontally and vertically) the genes responsible for their resistance to other bacteria [1, 20]. Resistant bacteria can be transferred from poultry products to humans via consuming or handling meat contaminated with pathogens [21]. Once these pathogens are in the human system, they could colonize the intestines and the resistant genes could be shared or transferred to the endogenous intestinal flora, jeopardizing future treatments of infections caused by such organisms [5, 22, 23, 24].
\nAntimicrobials’ use in animal production dates as far back as the 1910 when due to shortage of meat products, workers carried out protests and riots across America [25]. Scientists at that time started looking for means of producing more meat at relatively cheaper costs; resulting in the use of antibiotics and other antimicrobial agents [26]. With the global threat of antibiotic resistance and increasing treatment failures, the non-therapeutic use of antibiotics in animal production has been banned in some countries [8, 27, 28, 29]. Sweden is known to be the first country to ban the use of antimicrobials for non-therapeutic purposes between 1986 (for growth promotion) and 1988 (for prophylaxis) [27]. This move was followed by Denmark, The Netherlands, United Kingdom and other European Union countries [27]. These countries also moved a step further and banned the use of all essential antibiotics as prophylactic agents in 2011 [30].
\nSeveral other countries have withdrawn the use of some classes of antibiotics or set up structures that regulate the use of selected antibiotics in animal production [29]. Despite these developments, it is currently estimated that over 60% of all antibiotics produced are used in livestock production, including poultry [6, 31].
\nThe use of antibiotics in poultry and livestock production is favorable to farmers and the economy as well because it has generally improved poultry performance effectively and economically but at the same time, the likely dissemination of antibiotic resistant strains of pathogenic and non-pathogenic organisms into the environment and their further transmission to humans via the food chain could also lead to serious consequences on public health [32].
\nBacteria counteract the actions of antibiotics by four well-known mechanisms, namely; enzyme modification, alteration in target binding sites, efflux activity and decreased permeability of bacterial membrane [33]. This expression of resistance towards antibiotics by bacteria could either be intrinsic or acquired. Intrinsic resistance is due to inherent properties within the bacteria chromosome such as mutations in genes and chromosomally inducible enzyme production [34], whereas acquired resistance could be due to the transmission of resistance genes from the environment and/or horizontally transfer from other bacteria [35, 36].
\nThe bacterial genus
β-lactams were considered the first line of drugs for treatment of staphylococcal infections but due to emergence of high level of resistance to these and other drugs, there are currently very few drugs available for treatment of these infections [40]. Methicillin resistant
A study to detect the presence of MRSA in broilers, turkeys and the surrounding air in Germany reported the prevalence of MRSA in air as high as 77% in broilers compared to 54% in Turkeys. Ten different spa types were identified with spa type t011 and clonal complex (CC) 398 being the most prevalent. It was also found that for every farm, the same sequence types were present in both the birds and the environment [42]. This pattern of resistance was also reported in India with 1.6% of staphylococcal isolates containing mecA resistant gene [43].
\nIn Africa, studies carried out in Ghana and Nigeria have shown that livestock-associated
A study carried out in Ghana show that
Another study in Nigeria reported that the
In Pakistan, a study which investigated the causative agents for necropsy in chicken, recorded a 28% prevalence for
A study carried out on fecal isolates of
Pullorum disease in poultry is caused by the
Streptococcus is Gram-positive bacteria.
Resistance of
A study carried out by Elz’bieta and his colleagues, in their quest to compare the prevalence and genetic background of antimicrobial resistance in Polish strains of
Another study carried out in Kenya isolated thermophilic
It is a Gram-negative non-spore-forming rod, a psychrotrophic bacterium and able to survive and multiply at cold temperatures. Poultry meat is one of the most important sources of
High-dose penicillin-G remains sensitive to
A study in Egypt, identified 125 isolates of
Thirty strains of
In a study involving 18 strains of
A study in Bangladesh identified three
A study in Langa, South Africa identified 102 sub-species of
A study in Czech Republic identified 228 enterococcal isolates from the intestinal tract of poultry. These isolates were found to be highly resistant to tetracycline (80%), erythromycin (59%) and ofloxacin (51%) but exhibited low resistance to ampicillin (3%) and ampicillin/sulbactam (3%) [105]. A similar trend of resistance was reported among 163 Enterococcal isolates from poultry litter in the Abbotsford area of British Columbia, Canada. The identified enterococcal isolates were found to be highly resistant to lincomycin (80.3%), tetracycline (65.3%), penicillin (61.1%) but showed low resistance towards to nitrofurantoin (3.8%), daptomycin (3.5%) and gentamycin (0.8%) [108]. There is a high possibility of multi-drug resistant enterococci in animal meat and fecal matter being transferred to humans [106].
\nA study in Iran identified 54
A similar trend of antibiotic resistance was observed in 36
Infections from other bacterial species could also result in the use of antibiotics. These include Mycoplasmosis (caused by
Several bacterial species are the major causes of infections in poultry and other animal husbandry. Most of these infections are linked to foodborne outbreaks, live animal contact, poor hygiene, and environmental exposure. With the emergence of antimicrobial resistance, the pathogenicity and virulence of these organisms have increased and treatment options are diminishing and also more expensive. Multidrug resistant bacteria have been found in poultry, poultry products, carcasses, litter and fecal matter of birds and these pose a risk to both handlers, consumers and a threat to global and public health. The above information also calls for increased surveillance measures and monitoring of antibiotic usage in both animal husbandry and humans throughout the world.
\nIntechOpen’s Academic Editors and Authors have received funding for their work through many well-known funders, including: the European Commission, Bill and Melinda Gates Foundation, Wellcome Trust, Chinese Academy of Sciences, Natural Science Foundation of China (NSFC), CGIAR Consortium of International Agricultural Research Centers, National Institute of Health (NIH), National Science Foundation (NSF), National Aeronautics and Space Administration (NASA), National Institute of Standards and Technology (NIST), German Research Foundation (DFG), Research Councils United Kingdom (RCUK), Oswaldo Cruz Foundation, Austrian Science Fund (FWF), Foundation for Science and Technology (FCT), Australian Research Council (ARC).
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