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Unit 7: Microbial Genetics and Microbial Metabolism - Biology

Unit 7: Microbial Genetics and Microbial Metabolism - Biology


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The genome of prokaryotes is usually made ​​up of one ''chromosome'' and plasmids. Eukaryota however, contain a larger number of chromosomes - we distinguish two types of eukaryota's chromosomes (nuclear and mitochondrial) and sometimes even plasmids. Most of what we know about the chromosomes of prokaryotes have been obtained from studies of E.coli – it is the organism of choice for such research of prokaryotes. Chromosome consists of double–stranded circular DNA.

Thumbnail: Supercoiling of the DNA in E.Coli is credited to Garasone and is licensed via a Creative Commons Attribution 3.0 Czech Republic.


Brock Biology of Microorganisms, 16th edition

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Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

Keywords: Anthropogenic activities Groundwater Groundwater microbiome Land use Metagenomics analysis Microbial diversity.


HAZARD APPRAISAL AND CRITICAL CONTROL POINT (HACCP) | The Overall Concept

Predictive Microbiology

The synergy of these different factors is a complex one. Computer-based mathematical models have therefore been created that take into account the factors mentioned above. They allow for predictions being made concerning microbial kinetics in foods. This predictive microbiology is based on data obtained from broth cultures under standardized conditions. If such a programme is fed with data on a food’s intrinsic factors, on the atmospheric conditions of packaging, and on the projected time and temperature of storage, the prospective behaviour of a microbial species can be computed and depicted in graphs. However, owing to the complex composition of foods, the results from predictive microbiology can only provide a framework for the understanding of the ecology and kinetics of microorganisms in foods. In order to obtain exact data for a particular food, further testing is required. Storage trials are a suitable means of testing the behavior of certain microorganisms as long as the species in question can be found regularly in the food product under consideration. If this is not the case, challenge tests can be performed where foods or raw materials are spiked with pathogens.


Structure of DNA

The basic unit of DNA structure is a nucleotide, composed of phosphate deoxyribose sugar and a nitrogenous base (Plate 4 and 5). Each deoxyribose sugar bonds covalently in a repeating pattern with two phosphates. One of the bonds is to the number 5’ (read ‘five prime’) carbon on deoxyribose and the other is to the 3’ carbon which specifies the order and direction of each strand. This formation results in an elongate strand with a sugar-phosphate backbone.

The nitrogen bases, purines, and pyrimidines attach by covalent bonds at the 1’ position of the sugar. They span the center of the molecule and pair with appropriate complementary bases from the other strand, thereby forming a double-stranded helix.

The paired bases are so aligned as to be joined by hydrogen bonds. Such weak bonds are easily broken, allowing the molecule to be ‘unzipped’ into its complementary strands. This is important so as to gain access to the information encoded in the nitrogen base sequence.

It should be noted that the purine adenine (A) pairs with the pyrimidine thymine (T) and the purine guanine (G) pairs with the pyrimidine cytosine (C). And the adenine forms two hydrogen bonds with thymine and cytosine forms three hydrogen bonds with guanine. This AT and GC base pairing means that the two strands in a DNA double helix are complementary.

It should also be noted that the two strands of the DNA are not oriented in the same direction. One side of the helix runs in the opposite direction of the other, in what is called an antiparallel arrangement. The order of the bond between the carbon on deoxyribose and the phosphate is used to keep track of the direction of the two sides of helix. Thus, one helix runs from the 5’ to 3’ direction and the other runs from the 3’ to 5’ direction. This characteristic is a significant factor in DNA synthesis and translation.


Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism

The relationship between the number of available nutrients and community diversity is a central question for ecological research that remains unanswered. Here, we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.


Brock Biology of Microorganisms (PDF)

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Content of Brock Biology of Microorganisms 14th edition (PDF)

UNIT I: THE FOUNDATIONS OF MICROBIOLOGY

1. The Microbial World.

2. Microbial Cell Structure and Function.

3. Microbial Metabolism.

4. Molecular Information Flow and Protein Processing.

UNIT II: MICROBIAL GROWTH AND REGULATION

5. Microbial Growth and Its Control.

6. Microbial Regulatory Systems.

7. Molecular Biology of Microbial Growth

8. Viruses and Their Replication.

UNIT III: GENOMICS AND GENETICS

9. Microbial Systems Biology.

10. Viral Genomics.

11. Genetics of Bacteria and Archaea.

12. Biotechnology and Synthetic Biology.

UNIT IV: MICROBIAL EVOLUTION AND DIVERSITY

13. Microbial Evolution and Systematics.

14. Metabolic Diversity of Microorganisms.

15. Functional Diversity of Microorganisms.

16. Diversity of Bacteria.

17. Diversity of Archaea.

18. Diversity of Microbial Eukarya.

UNIT V: MICROBIAL ECOLOGY AND ENVIRONMENTAL MICROBIOLOGY

19. Taking the Measure of Microbial Systems.

20. Microbial Ecosystems.

21. Nutrient Cycles in Nature.

22. Microbiology of the Built Environment.

23. Microbial Symbioses with Microbes, Plants, and Animals.

UNIT VI: MICROBE-HUMAN INTERACTIONS AND THE IMMUNE SYSTEM

24. Microbial Symbioses with Humans.

25. Microbial Infection and Pathogenesis.

26. Innate Immunity: Broadly Specific Host Defenses.

27. Adaptive Immunity: Highly Specific Host Defenses.

28. Clinical Microbiology and Immunology.

UNIT VII INFECTIOUS DISEASES AND THEIR TRANSMISSION

29. Epidemiology.

30. Person-to-Person Bacterial and Viral Diseases.

31. Vectorborne and Soilborne Bacterial and Viral Diseases.

32. Foodborne and Waterborne Bacterial and Viral Diseases.

33. Eukaryotic Pathogens: Fungi, Protozoa, and Helminths.


Key Features

  • Explores microbial metabolic pathways in the human body and implications for disease
  • Investigates specific steps involved in metabolic reactions in the human microbiome, including shikimate pathways and tryptophan pathways
  • Considers a variety of diseases and disorders, such as Alzheimer’s disease, metabolic syndromes, Crohn’s disease and Covid-19
  • Includes analysis of various amino acids and enzymes in microbial and human cells and how these can impact health

Noisy metabolism can drive the evolution of microbial cross-feeding

Cross-feeding, the exchange of nutrients between organisms, is ubiquitous in microbial communities. Despite its importance in natural and engineered microbial systems, our understanding of how cross-feeding arises is incomplete, with existing theories limited to specific scenarios. Here, we introduce a novel theory for the evolution of cross-feeding, which we term noise-averaging cooperation (NAC). NAC is based on the idea that, due to their small size, bacteria are prone to noisy regulation of metabolism which limits their growth rate. To compensate, related bacteria can share metabolites with each other to “average out” noise and improve their collective growth. This metabolite sharing among kin then allows for the evolution of metabolic interdependencies via gene deletions (this can be viewed as a generalization of the Black Queen Hypothesis). We first characterize NAC in a simple model of cell metabolism, showing that metabolite leakage can in principle substantially increase growth rate in a community context. Next, we develop a generalized framework for estimating the potential benefits of NAC among real bacteria. Using single-cell protein abundance data, we predict that bacteria suffer from substantial noise-driven growth inefficiencies, and may therefore benefit from NAC. Finally, we review existing evidence for NAC and outline potential experimental approaches to detect NAC in microbial communities.


Brock Biology of Microorganisms [RENTAL EDITION] 16th edition

Rent Brock Biology of Microorganisms [RENTAL EDITION] 16th edition (978-0134874401) today, or search our site for other textbooks by Michael T. Madigan. Every textbook comes with a 21-day "Any Reason" guarantee. Published by Pearson.

This print textbook is available for students to rent for their classes. The Pearson print rental program provides students with affordable access to learning materials, so they come to class ready to succeed. For courses in general microbiology. Authoritative. Accurate. Accessible Brock Biology of Microorganisms sets the standard for accuracy, impeccable scholarship, a visually stunning art program, and the use of cutting edge research to illustrate basic concepts. The text guides students through the six major themes of microbiology — Evolution, Cell Structure and Function, Metabolic Pathways, Information Flow and Genetics, Microbial Systems, and the Impact of Microorganisms — as outlined by the American Society for Microbiology Conference on Undergraduate Education (ASMCUE). This robust and modern approach takes students through the genomics revolution and “omics” maze that has transformed microbiology and shares powerful tools that microbiologists use to probe deeper and further into the microbial world than ever before. The 16th Edition expands the extraordinary art program to ensure students experience microbiology as a visual science while providing an overview of the microbial world with basic principles that students all need to master. Each chapter’s theme focuses on a recent discovery that connects students with the most current science and engages them with exciting, real-world topics. Now available with Modified Mastering Microbiology By combining trusted author content with digital tools and a flexible platform, Mastering personalizes the learning experience and improves results for each student. Mastering Microbiology extends learning and provides students with a platform to practice, learn, and apply knowledge outside of the classroom.

0134874404 / 9780134874401 Brock Biology of Microorganisms [RENTAL EDITION], 16/e

UNIT 1: THE FOUNDATIONS OF MICROBIOLOGY

2. Microbial Cell Structure and Function

4. Microbial Growth and Its Control

5. Viruses and Their Multiplication

UNIT 2: MOLECULAR BIOLOGY AND GENETICS

6. Microbial Information Flow and Protein Processing

7. Microbial Regulatory Systems

8. Molecular Aspects of Microbial Growth

9. Genetics of Bacteria and Archaea

UNIT 3: GENOMICS, SYNTHETIC BIOLOGY, AND EVOLUTION

10. Microbial Genomics and Other Omics

11. Viral Genomics and Diversity

12. Biotechnology and Synthetic Biology

13. Microbial Evolution and Genome Dynamics

UNIT 4: MICROBIAL DIVERSITY

14. Metabolic Diversity of Microorganisms

15. Ecological Diversity of Bacteria

16. Phylogenetic Diversity of Bacteria

17. Phylogenetic Diversity of Archaea

18. Diversity of Microbial Eukarya

UNIT 5: MICROBIAL ECOLOGY AND ENVIRONMENTAL MICROBIOLOGY

19. Taking the Measure of Microbial Systems

22. Microbiology of the Built Environment

23. Microbial Symbioses with Microbes, Plants, and Animals

UNIT 6: MICROBE—HUMAN INTERACTIONS AND THE IMMUNE SYSTEM

24. Microbial Symbioses with Humans

25. Microbial Infection and Pathogenesis

26. Innate Immunity: Broadly Specific Host Defenses

27. Adaptive Immunity: Highly Specific Host Defenses

28. Immune Disorders and Antimicrobial Therapy

UNIT 7: INFECTIOUS DISEASES

29. Diagnosing Infectious Diseases

30. Epidemiology and Public Health

31. Person-to-Person Bacterial and Viral Diseases

32. Vectorborne and Soilborne Bacterial and Viral Diseases

33. Waterborne and Foodborne Bacterial and Viral Diseases

34. Eukaryotic Pathogens: Fungi, Protozoa, and Helminths

Lisa A. Urry, Lisa Urry, Michael Cain, Michael L. Cain, Steven Wasserman, Steven A. Wasserman, Peter V. Minorsky, Peter Minorsky, Jane B. Reece, Jane Reece

Microbiology: An Introduction (13th Edition)

Gerard J. Tortora, Gerard Tortora, Berdell R. Funke, Berdell Funke, Christine L. Case, Christine Case, Derek Weber, Warner Bair, Warner Bair III

Martha Taylor, Martha R. Taylor, Eric J. Simon, Eric Simon, Jean Dickey, Jean L. Dickey, Kelly Hogan, Kelly A. Hogan, Jane B. Reece, Jane Reece

Visualizing Human Biology

Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson

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Watch the video: Microbiology Genetics Chapter 8 Part I (October 2022).