Microbial Ecosystems

Ecosystems

A community of organisms living in a specified area, interacting with each other and the environment

Biotic factors

Other organisms affecting ecosystem

Abiotic factors

Minerals, gases and water in ecosystem

Primary producers

Capture energy through photosynthesis

Consumers

Heterotrophic organisms - ingest/utilize stored photosynthetic energy

Decomposers

Recycle components back into environment

Niche

Specific function of an organism within an ecosystem

Biofilms

Groups/laters of microbes on a surface that interact with and support each other like plaque

Primary colonizers

Forms often with appendages bacteria (reproduced by budding) forming the primary later on a surface

Exopolysaccharide (EPS)

Helps protect the biofilm but also helps form water-filled channels for transport of nutrients and wastes

Direct sequencing

Without grown or cloning, use sample DNA as template for PCR using SSU rRNA gene primers and sequencing. Sequences compared to databases of known sequences for identification (GenBank = public database)

Denaturing gradient gel electrophoresis (DGGE)

Indirect method for characterizing microbial ecosystems. Can illustrate larger-scale differences in DNA sequences without identifying base. Also, Ca==

Terminal restriction fragment length polymorphism (TRFLP)

Provides a profile of the diversity and relative abundance (fluorescence intensity) of different microbes present in the sampe

Metagenomics

DNA from an environment sample is used to construct a genomic library

In sequence-driven analysis

DNA is extracted and squared. Bioinformatics tools are used to assembly and annotate the sequences, identifying genes and their potential roles

In function driven analysis

DNA from the sample is fragmented and cloned into a host organism (e.g. bacteria). The host organisms are screened for specific functions (enzyme activity), the corresponding gene is sequenced and analyzed

Oligotrophy

Using nutrients at very low concentrations

Dead zones

Areas without enough oxygen to support much eukaryal

Epilimnion

Warmer aerobic upper level

Hypolimnion

Colder aerobic upper level

Thermocline

Layer in the middle of epilimnion and hypolimnion

Biomes

Categories of ecosystems based on vegetation characteristics

Soils

Form through microbial decomposition of plant and animal matter. Contains more microbial diversity than any other microbial ecosystems. Combine with abiotic minerals and excreted nutrients from plant roots.

Lignin/lignocellulose

Macromolecule of covalently linked phenolic-alcohol molecules

Rhizosphere

The area of soil immediately surrounding plant roots possessing large amounts of organic carbon due to root’s exudate (sugars, amino acids, other organics)

Basidiomycetes

Two types; white rot and brown rot. Specialize in breaking down lignocellulose

Actinomycetes

Bacteria that are good at degrading much of the plant organic matter, providing them with ample nutrients

Bioremediation

The use of microbes to consume and remove human-made materials from soil.

Xenobiotics

Chemicals not normally found in nature

Biostimulation

Oxygen and limiting nutrients are provided in abundance to promote microbe activity

Cometabolism

Involves addition of a nutrient that stimulates a broad substrate-range degradation pathway

Bioaugmentation

Involves specific addition of a known degrading microbe to a contained environment

Deep subsurface microbiology

Microbes have been discovered in deep-sea vents, hot springs, oil wells and goldmine subterranean rock.

Hydrothermal vents

Best studied deep area (ocean floor) microbial community types

Terrestrial hot springs

Milder temperatures (mid 70), neutral pH, access to sunlight. Primary production from cyanobacteria, which create thick biofilm mat in the upper layers