ENVE 176: Microbial Biology for Environmental Engineers
Estimated study time: 10 minutes
Table of contents
Sources and References
Primary texts — Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., and Stahl, D. A., Brock Biology of Microorganisms; Rittmann, B. E. and McCarty, P. L., Environmental Biotechnology: Principles and Applications.
Supplementary texts — Metcalf & Eddy, Wastewater Engineering: Treatment and Resource Recovery; Willey, J. M., Sandman, K., and Wood, D., Prescott’s Microbiology; Maier, R. M. and Pepper, I. L., Environmental Microbiology.
Online resources — MIT OpenCourseWare 1.018J Fundamentals of Ecology and 7.014 Introductory Biology; NCBI Bookshelf open microbiology texts; Joint Genome Institute (JGI) genome portal public resources; EMBL-EBI bioinformatics training materials; US EPA Method 1604 and microbial water quality guidance.
Chapter 1: Microbes and Their World
Microbes — bacteria, archaea, fungi, protists, and viruses — run the biogeochemistry of the planet. Environmental engineers harness, direct, or contain their activity in treatment plants, remediation systems, and monitoring programs. A solid grasp of microbial structure, physiology, and diversity is essential.
1.1 Scope and Scales
Microorganisms span sizes from \(20\ \text{nm}\) viruses to \(500\ \mu\text{m}\) filamentous bacteria. Their biomass rivals that of plants; their collective metabolic capacity includes virtually every energy-yielding reaction thermodynamically feasible on Earth. Engineering systems — aeration tanks, anaerobic digesters, drinking-water filters — are designed to cultivate or suppress specific microbial communities.
1.2 Three Domains of Life
Carl Woese’s molecular phylogeny established three domains: Bacteria, Archaea, and Eukarya. Archaea include extremophiles and methanogens central to anaerobic treatment. Eukaryotic microbes (fungi, algae, protozoa) contribute to wastewater treatment and cause waterborne diseases.
Chapter 2: Cell Structure and Function
2.1 The Bacterial Cell
A typical bacterial cell contains a cytoplasmic membrane (phospholipid bilayer with proteins), cytoplasm with ribosomes and a single circular chromosome, and often plasmids. External structures include the peptidoglycan cell wall (thick in Gram-positive, thin in Gram-negative with an outer membrane), capsules or slime layers (biofilm formation), flagella (motility), and pili (adhesion, conjugation).
2.2 Membrane Transport and Energetics
Active transport moves solutes against gradients using ATP or proton-motive force (PMF). The PMF combines a pH gradient and a membrane potential:
\[ \Delta p = \Delta\psi - \frac{2.3\,RT}{F}\,\Delta\mathrm{pH} \]and powers ATP synthesis via ATP synthase, flagellar rotation, and symport/antiport.
2.3 Archaeal Specializations
Archaeal membranes use ether-linked isoprenoid lipids, often with monolayer structures that stabilize cells under high temperature or low pH. Cell walls use pseudopeptidoglycan or S-layers. These adaptations allow archaea to dominate environments from hydrothermal vents to hypersaline brines.
Chapter 3: Cultivation and Characterization
3.1 Growth Requirements
Culture media provide carbon, nitrogen, phosphorus, trace elements, and, for heterotrophs, a reduced carbon source. Oxygen requirements span obligate aerobes, facultative anaerobes, microaerophiles, aerotolerant anaerobes, and obligate anaerobes (which often use alternative terminal electron acceptors). Temperature optima define psychrophiles, mesophiles, thermophiles, and hyperthermophiles.
3.2 Growth Kinetics
In batch culture, a population grows exponentially during the log phase:
\[ X(t) = X_0 e^{\mu t} \]with specific growth rate \(\mu\). At low substrate concentration \(\mu\) depends on substrate by the Monod equation:
\[ \mu = \mu_{\max}\,\frac{S}{K_S + S} \]Biomass yield \(Y = \Delta X/\Delta S\) ties growth to substrate consumption. The inverse of the mean residence time in a chemostat equals the dilution rate, which at steady state equals \(\mu\), producing
\[ S = \frac{K_S\,D}{\mu_{\max} - D} \]a workhorse relation in reactor engineering.
3.3 Cultivation-Independent Characterization
Because most environmental microbes are not cultivable on standard media — the great plate count anomaly — engineers increasingly rely on molecular methods. DNA extraction, PCR amplification of the 16S rRNA gene, and high-throughput sequencing characterize communities without cultivation. Fluorescence in situ hybridization (FISH) uses fluorescent probes targeting rRNA for in situ visualization.
Chapter 4: Genetics, Phylogeny, and Taxonomy
4.1 Genome Organization
Bacterial chromosomes are typically a single circular DNA molecule of \(0.5\text{–}10\ \text{Mbp}\). Plasmids carry accessory genes (antibiotic resistance, catabolic pathways, virulence). Gene expression is regulated via operons — clusters of genes under a single promoter, such as the \(lac\) operon.
4.2 Horizontal Gene Transfer
Transformation (uptake of free DNA), conjugation (plasmid transfer via pili), and transduction (viral-mediated transfer) allow genes to move between lineages. Horizontal gene transfer accelerates adaptation and complicates phylogenetic reconstruction.
4.3 Phylogenetic Inference
Phylogenies are reconstructed from conserved gene alignments (classically 16S rRNA) using maximum-likelihood or Bayesian methods. Operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) cluster sequences at a similarity threshold; taxonomy assigns names against curated databases (SILVA, GTDB, Greengenes).
4.4 Taxonomy for Engineering
Wastewater engineers care about specific taxa: ammonia oxidizers (Nitrosomonas), nitrite oxidizers (Nitrospira), denitrifiers, polyphosphate-accumulating organisms, methanogens (Methanosaeta, Methanosarcina), filamentous bulking organisms. Knowing who is doing what in a reactor guides troubleshooting and design.
Chapter 5: Metabolic and Genetic Diversity
5.1 Energy Metabolism
Chemoorganotrophs oxidize organic compounds; chemolithotrophs oxidize inorganic electron donors (H\(_2\), NH\(_3\), NO\(_2^-\), Fe\(^{2+}\), S\(^{2-}\)); phototrophs harvest light. Electron acceptors range from O\(_2\) through NO\(_3^-\), Mn(IV), Fe(III), SO\(_4^{2-}\), to CO\(_2\), with standard potentials decreasing in that order. Free-energy yields decline along this series, defining the redox ladder observed in aquifers and sediments.
5.2 Carbon Metabolism
Glycolysis, the TCA cycle, and oxidative phosphorylation produce ATP and reducing equivalents in aerobic heterotrophs. Fermentation pathways generate ATP under anaerobic conditions, with organic products (lactate, ethanol, acetate, butyrate, H\(_2\), CO\(_2\)) depending on the organism. Methanogenesis from acetate or H\(_2\)/CO\(_2\) completes anaerobic digestion.
5.3 Nitrogen Metabolism
Nitrification oxidizes ammonia to nitrate in two steps, historically by Nitrosomonas and Nitrobacter, now known also to proceed through comammox Nitrospira. Denitrification reduces nitrate to N\(_2\). Anammox (anaerobic ammonium oxidation) couples \(\mathrm{NH_4^+}\) and \(\mathrm{NO_2^-}\) to produce N\(_2\), with substantial energy and aeration savings when exploited in partial-nitritation/anammox reactors.
Chapter 6: Genomics, Bioinformatics, and Pathogenesis
6.1 Genomics and Metagenomics
Whole-genome sequencing of isolates reveals full metabolic potential. Metagenomics sequences community DNA directly, reconstructing metagenome-assembled genomes (MAGs) from environmental samples. Metatranscriptomics and metaproteomics reveal what genes are expressed.
6.2 Bioinformatics Tools
Engineers interact with tools including BLAST (sequence similarity), QIIME 2 and mothur (amplicon analysis), SPAdes and MEGAHIT (assembly), MetaBAT (binning), Prokka (annotation), KEGG (metabolic pathways). Results support rational design of treatment processes, bioaugmentation, and monitoring programs.
6.3 Pathogens and Public Health
Water-borne pathogens include bacteria (Escherichia coli, Salmonella, Campylobacter, Legionella), viruses (noroviruses, rotaviruses, enteroviruses, SARS-CoV-2 in wastewater surveillance), and protozoan (oo)cysts (Giardia, Cryptosporidium). Indicator organisms (E. coli, enterococci) serve as tractable surrogates for faecal contamination. Disinfection — chlorination, ozonation, UV — and physical removal (filtration, membranes) combine to achieve required log-removal values.
6.4 Biofilms and Engineered Communities
Microbes overwhelmingly live attached in biofilms, embedded in self-produced extracellular polymeric substances. Biofilms dominate engineered systems: fixed-film biological reactors, biofilters, membrane biofilm reactors, drinking-water distribution surfaces. They confer protection against disinfection and predation, which can be engineered to advantage or represent a treatment challenge.
This course lays down the biological literacy needed to engineer with, rather than around, the microbial world that runs the biogeochemistry of our water, air, and soil.
