🧬 What is a Species?

Species can be defined in several ways depending on the organism:

• Animals: easy — if they can mate and have fertile offspring, same species.
• Bacteria: they don’t mate — they divide! So, scientists use genetic similarity.

🔹 OTUs vs ASVs

• OTU (Operational Taxonomic Unit): groups sequences that share ≥97.5% similarity in a marker gene (like 16S rRNA).
• ASV (Amplicon Sequence Variant): much higher precision — unique DNA variants, usually 99% similarity cutoff for species-level resolution. 👉 ASVs are preferred today because they treat every unique sequence separately before comparing them to databases.

🔹 How Do We Confirm Species?

If full genomes are available:

• Use ANI (Average Nucleotide Identity) → Species = ≥95% identity across the genome → Small gene differences (e.g., from horizontal gene transfer) still count as same species.

🦠 Example: E. coli — same species, but thousands of strains, some harmless, some pathogenic because of different genes.

🌍 How Fast Do Species Evolve?

Speciation in bacteria happens slowly but measurably:

• Through gene transfer, mutations, and selection.
• Some lab studies show gene transfer events within days when microbes are mixed — but most don’t persist.
• Over evolutionary time, this diversification leads to new species.

Sequencing entire environmental communities (metagenomics) lets scientists reconstruct genomes to track these changes — though contamination between nearly identical strains can make this tricky.

💻 The MiDAS Field Guide

MiDAS (Microbial Database for Activated Sludge) is a global open resource for studying wastewater microbes. It provides:

• 🧫 33,000+ identified species
• 🌐 Data on distribution, abundance, and function
• 🔍 Searchable taxonomy browser for phylum → species
• 📈 Tools to visualize abundance or traits (filamentous, hydrophobic, etc.)
• 🧪 Protocols and definitions for cell traits, metabolism, and sequencing methods
• 🧠 Links to antibiotic resistance genes (ARGs), genome data, and publications.

Example:

If you search Microthrix:

• You see it’s aerobic, filamentous, hydrophobic, and known to cause foam problems in treatment plants.
• You can view FISH probes, genome access, and its global abundance across plant types and countries.

💊 Antibiotic Resistance in Wastewater

• Many systems are thought to be “hotspots” for ARG exchange — but Danish studies show limited evidence.
• Some bacteria naturally carry ARGs because they evolved to defend against environmental antibiotics.
• However, potential transfer to pathogens remains a global concern.

🧫 Global Patterns of Bacteria in Wastewater

MiDAS studies compare wastewater microbiomes worldwide:

• Different plants share many genera, but not the same species.
• The same treatment process (carbon removal, phosphorus removal, etc.) in two plants may have different microbial communities.
• Reasons: local environment, temperature, industrial inputs, and immigration of bacteria from incoming wastewater.

🌱 Community Assembly Theory

Why do certain bacteria dominate in one plant and not another?

Deterministic Factors (🧩 measurable)

• Temperature
• Substrates (available nutrients)
• Environmental conditions
• Interactions (competition, cooperation)

→ These define selection or niche occupation.

Stochastic Factors (🎲 random)

• Dispersal (immigration): bacteria coming in from air, soil, or wastewater inflow
• Drift: random survival or extinction of species
• Speciation: new variants forming by mutation/adaptation over time

Together they shape community structure — the microbial composition of each treatment plant.

💭 The “Everything Is Everywhere” Hypothesis

Engineers once believed:

“All bacteria exist everywhere — give them the right conditions, and the right ones will grow.”

But… studies disagree.

🔹 Evidence for:

• Bacteria spread easily through water, air, and waste.
• With similar environments, the same functions can appear.

🔹 Evidence against:

• Local conditions matter — Greenland ≠ Sahara.
• Microbes entering plants differ regionally.
• Some genera are universal, but specific species are not.
• Even in Denmark, Aalborg vs. Copenhagen plants have distinct bacterial profiles.

Conclusion: Not everything is everywhere. Immigration sources strongly influence which microbes establish.

🚰 Sewer Systems as Microbial Sources

Researchers studied sewer microbiomes and discovered:

• Sewers are major microbial incubators.
• Many key bacteria already grow in sewer biofilms before reaching the treatment plant.
• Incoming wastewater renews 5–10% of biomass daily, but ~70% of incoming microbes die quickly (often human-associated gut bacteria).
• The important bacteria — those driving treatment processes — originate from the sewer biofilms, not from the raw wastewater.

➡️ So, the sewer + treatment plant act as one integrated ecosystem.

🧩 Key Takeaways

🧠 Summary Mnemonic

S.P.E.C.I.E.S.

• Sequencing defines microbes
• Plants differ globally
• Everything’s not everywhere
• Conditions + chance shape communities
• Immigration from sewers matters
• Evolution is slow
• Sewer systems = source ecosystems