microbial phylogenetics

Examples of microbial phylogenetics in the following topics:

• Phylogenetic Analysis

  • The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.
  • Microbial phylogenetics is the study of the evolutionary relatedness among various groups of microorganisms.
  • The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.
  • There are four steps in general phylogenetic analysis of molecular sequences: (i) selection of a suitable molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple sequence alignment (MSA), and (iv) phylogenetic treeing and evaluation.
  • Multilocus sequence analysis (MLSA) represents the novel standard in microbial molecular systematics.

• Environmental Diversity of Microbes

  • The microbial world encompasses most of the phylogenetic diversity on Earth, as all Bacteria, all Archaea, and most lineages of the Eukarya are microorganisms.
  • In turn, the environment and the recent temperature anomalies play a crucial role in driving changes to the microbial communities.
  • For microbiologists, it is critical to study microbial adaptation to different environments and their function in those environments to understand global microbial diversity, ecology, and evolution.
  • Interfering with natural microbial biomass disrupts the balance of nature and the ecosystem and leads to loss of biodiversity.
  • Summarize how microbial diversity contributes to microbial occupation of diverse geographical niches.

• Nucleic Acid Sequencing and rRNA Analysis

  • The 16SrRNA gene is used for phylogenetic studies, as it is highly conserved between different species of bacteria and archaea.
  • Unfortunately, while primers can be defined to amplify this gene from single genomes, this method is not accurate enough to estimate the diversity of microbial communities from their environments.
  • Paradoxically, methodological denial is now a rule in published articles that use 16S rRNA gene amplicon surveys to study unknown microbial communities.
  • Describe how the 16SrRNA gene can be used for phylogenetic studies and in medical microbiology for bacterial identification

• Alphaproteobacteria

  • Aerobic anoxygenic phototrophic bacteria are alphaproteobacteria, widely distributed marine plankton that may constitute over 10% of the open ocean microbial community.
  • Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria with the exception of Betaproteobacteria and Gammaproteobacteria.

• Shared Features of Bacteria and Archaea

  • In phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria.

• Diagnosing Microbial Diseases

  • The methods used to diagnose microbial disease include microbial culture, microscopy, biochemical tests, and molecular diagnostics.
  • The first tool in diagnosing microbial disease is microbial cultures.
  • An additional tool utilized for microbial disease diagnosis is microscopy.
  • Biochemical tests are also used to help in microbial disease diagnosis.
  • Compare and contrast the various methods used to diagnose microbial diseases: microbial culture, microscopy, biochemical tests and molecular diagnostics

• Viral Genomes in Nature

  • As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria and archaea, and 18S RNA for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics.
  • They infect and destroy the bacteria in aquatic microbial communities, comprising the most important mechanism of recycling carbon in the marine environment.

• Methanogenesis

  • They have been identified only from the domain Archaea - a group that is phylogenetically distinct from eukaryotes and bacteria - though many live in close association with anaerobic bacteria.
  • The production of methane is an important and widespread form of microbial metabolism, and in most environments, it is the final step in the decomposition of biomass.

• Low Temperatures

  • Low temperatures usually inhibit or stop microbial growth and proliferation but often do not kill bacteria.
  • Temperature is an important factor for microbial growth.
  • Human microbial pathogens usually thrive at body temperature, 37ºC.
  • Low temperatures usually inhibit or stop microbial growth and proliferation but often do not kill bacteria.
  • Refrigeration is also used to facilitate the preservation of liquid medicines or other substances used for research where microbial growth is undesirable, often combined with added preservatives.

• Limitation of Microbial Growth by Nutrient Supply

  • Nutrients are necessary for microbial growth and play a vital role in culturing microorganisms outside of their natural environment.
  • Nutrients are necessary for microbial growth and play a vital role in the proper cultivation of microorganisms in the laboratory and for proper growth in their natural environments.
  • In industrial microbiology this concept is critical, as microbial growth and production is dictated by proper cellular growth and metabolism.
  • Describe the role of nutrients in microbial growth and their culture in the lab