Microbial Ecology I PDF

CHAPTER 21.1 21.3 Microbial Ecology Copyright © 2024 by W. W. Norton & Company, Inc. Introduction § Microbes have evolved to colonize every habitat of our biosphere § Within an animal, a microbial community can provide essential components for its host 2 Microbial Communities: Omics Analysis Introdu...

CHAPTER 21.1 21.3 Microbial Ecology Copyright © 2024 by W. W. Norton & Company, Inc. Introduction § Microbes have evolved to colonize every habitat of our biosphere § Within an animal, a microbial community can provide essential components for its host 2 Microbial Communities: Omics Analysis Introduction § A population is a group of individuals of one species living in a common location. 5 Introduction § A population is a group of individuals of one species living in a common location. § The sum of all the populations of different species constitute a community. 6 Introduction § A population is a group of individuals of one species living in a common location. § The sum of all the populations of different species constitute a community. § An ecosystem consists of populations of species plus their habitat or environment. 7 21.1 Microbial Communities: Metagenomes § A metagenome is the sum of all DNA sequenced from an environmental sample. 8 21.1 Microbial Communities: Metagenomes § A metagenome is the sum of all DNA sequenced from an environmental sample § rRNA sequences are the standard for identifying environmental taxa 9 21.1 Microbial Communities: Metagenomes and Single-Cell Sequencing § Today, with advanced sequencing technologies, we are addressing exciting questions: Who is there? What do their genomes represent? What are they doing? How do the communities vary under different conditions? 10 Analyzing a Metagenome § Sampling requires that we first define a target community to study. 11 Analyzing a Metagenome – 2 § Once the community has been sampled, researchers then must: Separate the microbes from their physical environment Break open the cells Isolate the DNA 12 DNA sequences are reported in fragments 13 Illumina sequencing Metagenome Sequencing and Assembly § Genome assembly of overlapping fragments (reads) into contigs. 16 Sequence Reads are Assembled into Scaffolds 17 The Deepwater Horizon Spill 18 The Deepwater Horizon Spill 19 The Deepwater Horizon Spill § To determine which microbes in the community possessed the ability to degrade petrolium researchers analyzed: Metagenomes derived from the community to look for the presence of genes encoding enzymes that can degrade hydrocarbons Metatranscriptomes to study the expression of RNA transcripts related to these pathways 20 The Deepwater Horizon Spill: Metagenomes, Metatranscriptomes 21 The Deepwater Horizon Spill: Metagenomes, Metatranscriptomes 22 Culturing the Uncultured § Metagenomics is our most powerful tool to identify the microbes that inhabit an ecosystem. Can learn who is there AND their functional potential 23 Culturing the Uncultured § Metagenomics is our most powerful tool to identify the microbes that inhabit an ecosystem. § Yet serious limitations remain. Metagenomes may miss community members. ― These may represent organisms of the “rare biosphere” § Novel “out-of-the-box” approaches to culturing can now reveal organisms previously missed or thought unculturable. 24 21.2 Functional Ecology § All organisms depend, directly or indirectly, on the presence of other organisms. 25 21.2 Functional Ecology § Within a community, each population of organisms fills a specific niche. A set of conditions, including habitat, resources, and relations with other species of the ecosystem, that enable an organism to grow and reproduce Organisms perform niche construction by shaping the biochemical dimensions of their habitat. 26 All Ecosystems Require Microbes § Dutch microbiologist Cornelius B. van Niel proposed two hypotheses of microbial ecology: 1. Every molecule existing in nature can be used as a source of carbon or energy by a microorganism somewhere. 2. Microbes are found in every environment on Earth. 27 The Food Web Represents The Flow Of Energy And Matter Through An Ecosystem § Levels of consumption are called trophic levels. 28 Carbon Assimilation and Dissimilation: The Food Web § Every food web depends on primary producers for two things: 1. Absorbing energy from outside the ecosystem 2. Assimilating minerals into biomass 29 Carbon Assimilation and Dissimilation: The Food Web § In addition, all ecosystems have consumers: Grazers and predators 30 Microbes within Food Webs: Producers to Decomposers 31 21.3 Symbiosis § One of the most fascinating results of evolution is how organisms adapt to the presence of others. § The most intimate association between organisms of different species is called symbiosis § Symbiotic associations include a full range of both positive and negative relationships. ― Whether positive or negative, both partners evolve in response to each other. 32 Organism 2 Fitness effect on partner: Organism 1 Organism 2 Fitness effect on partner: mutualism Organism 1 Mutualism: both organisms benefit from the relationship (two organisms grow in an intimate species-specific relationship in which both partner species benefit and may fail to grow independently) Mutualism Involves Partner Species That Require Each Other § Mutualism can involve two or more microbial partners. § Removal of the microbial partner leads to death or decreased growth of the host. § A highly evolved form of mutualism is the lichen. 35 Insects Possess Intracellular Bacteria § Most insects possess intracellular bacteria, inherited from mother to offspring. § Bacteria provide essential nutrients and may also defend the host § Host provides numerous functions lost from the bacteria by degenerative evolution. 36 Organism 2 Fitness effect on partner: mutualism synergism Organism 1 Synergism: both species benefit through growth, but the partners are easily separated and either partner can grow independently of the other Methanogens In The Gut Are Synergistic With Their Host Methanogens use the hydrogen and carbon dioxide produced from bacterial fermentations They help regulate hydrogen levels which increases the efficiency of beneficial gut microbes 38 Organism 2 Fitness effect on partner: commensalism Organism 1 commensalism Commensalism: One species benefits, while the partner species neither benefits nor is harmed (neutral) Beggiatoa Are Commensals With Their Community Members Oxidize hydrogen sulfide for energy Hydrogen sulfide is toxic for some bacteria Removal of this hydrogen sulfide enables the growth of other bacteria The other bacteria are not known to benefit Beggiatoa 40 Organism 2 Fitness effect on partner: parasitism Parasitism: One species (the parasite) benefits at the expense of the other (the specific host). Organism 1 parasitism “The relationship is usually obligatory for the parasite” Legionella pneumophilia Parasitizes Amoeba in Aquatic Environments 42 Legionella pneumophilia parasitizes macrophages in humans 43 Organism 2 Fitness effect on partner: amensalism Amensalism: One species benefits by harming others. The relationship is nonspecific. Organism 1 amensalism Meaning no specific host is needed. Streptomyces Release Antibiotics to Lyse Other Bacteria for Nutrients 45