Microbe-environment interactions: N/S/C cycles; soil/gut/ocean microbiomes; biofilms; quorum-sensing; metagenomics; phage-host; extremophiles; syntrophy; community-function.
Microbial Ecology
Microbial nitrogen cycle
N2 fixation (nif), nitrification (amoA, nxr), denitrification (nar, nir, nor, nos), anammox; microbes mediate all major N transformations…
Microbial sulfur cycle
Dissimilatory sulfate reduction (dsrAB), sulfide oxidation (sox), elemental S disproportionation; deep-sea vents and Black Sea exemplify…
Microbial carbon cycle
Methanogens (mcrA), methanotrophs (pmoA, mmoX), CO2 fixation pathways (Calvin, rTCA, Wood-Ljungdahl, 3HP); microbes drive about half of…
Soil microbiome
Soil contains 10^9 to 10^10 cells per gram with thousands of operational taxonomic units; the Earth Microbiome Project (Thompson 2017)…
Gut microbiome (ecological view)
Human gut hosts 10^13 to 10^14 cells dominated by Firmicutes and Bacteroidetes; Human Microbiome Project 2012 baseline; functional…
Ocean microbiome (Prochlorococcus)
Prochlorococcus marinus is the most abundant photosynthetic organism (about 3 x 10^27 cells globally); discovered by Chisholm 1988; drives…
Biofilm formation
Attachment, microcolony, maturation, dispersal; EPS matrix protects cells; biofilms cause 80 percent of chronic infections (NIH estimate).
Quorum sensing
AHL (LuxI/LuxR) in gram-negative, AIP in gram-positive, AI-2 (LuxS) cross-species; cell-density-dependent collective gene regulation.
Shotgun metagenomics
Direct DNA sequencing of environmental samples without isolation; assembly into metagenome-assembled genomes (MAGs); Tyson 2004 first MAG…
Microbial phage-host dynamics
Lytic vs lysogenic cycles; kill-the-winner Lotka-Volterra-like dynamics; phages outnumber bacteria 10 to 1 in oceans; CRISPR-Cas immunity…
Extremophile environments
Thermophiles (Pyrolobus to 113 C), psychrophiles, halophiles, acidophiles, piezophiles; expand habitable-zone definitions and astrobiology…
Microbial syntrophy
Obligate metabolic cross-feeding (e.g. propionate oxidation by Syntrophobacter coupled to methanogenesis) is thermodynamically possible…
r vs K selection (microbial)
MacArthur-Wilson 1967 r/K theory applied to microbes: r-strategists (rapid growth, high mortality, copiotrophs like E. coli) vs…
Bacterial consortia + cross-feeding
Wintermute-Silver 2010 Acinetobacter-E.coli cross-feeding via amino-acid auxotrophy; basis of synthetic-microbial-community engineering;…
Antibiotic resistance evolution (eco)
WHO 2019 estimates 700k deaths/yr from AMR; selection-pressure from clinical + agricultural antibiotic use drives plasmid-mediated…
Methanogen + rumen / wetland microbiome
Methanogenic archaea (Methanobrevibacter, Methanosarcina) reduce CO2 + H2 -> CH4; rumen + wetland + landfill emissions are major…
Chemolithotroph energy budget
Chemolithotrophic bacteria (Nitrobacter, Thiobacillus, Acidithiobacillus) extract energy from inorganic redox couples; foundation of…
Kill-the-winner (Thingstad)
Thingstad-Lignell 1997 / Thingstad 2000: viral lysis preferentially kills most abundant prokaryotes; maintains diversity in marine…