MBIO162 Microbial Diversity

04 February 2025: Microbial Diversity I

What are microbes?

Microscopic - too small to be seen easily with the naked eye, ex. less than 1 mm. But some ‘microorganisms’ are arge enough to see with the naked eye

Some scientists would argue that the distinguishing features of microorganisms are small size, unicellular organization, and feeding by osmotrophy

But this would exclude many microscopic unicellular protists that feed by phagotrophy and the many mixotrophic protists that switch between photosynthesis (like plants) and phagotrophy (like animals)

Viruses are microscopic are not cellular.

So, the term ‘microbes’ encompasses all microscopic cellular organisms (i.e. bacteria, archaea, unicellular protists and fungi), together with the viruses

Numbers

Microbes have been on Earth for 3.8 billion (3.8 x 109) years

Age of the Earth is approximately 4.5 billion years

Over 5 x 1030 bacteria, archaea and protists

that’s 5 million, million, million, million, million

Major proportion of biomass on the planet

Over 1031 viruses – enough to span 100 times the distance across our galaxy

You are made of 10 times more microbial cells than human cells

Origin and evolution of life

The common pathway for the flow of information suggests that all living organisms share a common ancestor

Almost all the major evolutionary events occurred in the distant past

Evolution of life on Earth

Timeline

Earth formed 4.5 bya

Oceans of liquid water about 4 bya

Cellular organisms are thought to have evolved by 3.8 billion yrs, evidenced by ‘bacteria-like’ microfossils

Microbial formations called stromatolites can be found in rocks younger than 3.5 billion yrs

Primordial soup

Experiments have shown that organic precursors can be formed under certain conditions

We now think that surface conditions on early Earth were too hostile (great temperature fluctuations, meteor impacts, intense UV) for early evolution of life

Hydrothermal vents

Life arose from gases (H2, CO2, N2, and H2S) with energy from harnessing geochemical gradients created at a special kind of deep-sea hydrothermal vent

Containing tiny interconnected compartments or pores

Vent provide a steady and abundant supply of energy available in the form of reduced compounds (ex. H2 and H2S)

Compartments or inorganic vesicles created in alkaline deep sea vents could have produced chemical gradients very similar to the proton gradients seen in the membranes of all organisms today (chemiosmosis)

Used to drive synthesis of ATP or simpler equivalents

Were the first self-replicating molecules RNA?

We know that RNA can have catalytic properties

As different proteins emerged, some may have taken over the catalytic role of RNAs

DNA may then have taken over the role as repository of coding information (as it is more stable)

This three-part system became fixed early on and controls information processing in all life today

Lipid membranes: the origin of cells

Synthesis of phospholipid vesicles could have enclosed the replication and biochemical reactions

LUCA (last universal common ancestor) – a population of primitive cells

Life then diverged in two distinct directions, perhaps due to physicochemical differences in their niche

Natural selection led to the two lineages – Bacteria and Archcea becoming ever more distinct

Microbe classification, evolution and diversity

Domains:

Bacteria and Archaea

Both feed by absorption of nutrients

Eukarya

Protists

Different types, feed by engulfing particles or other organisms or by photosynthesis (or both)

E.g. flagellates, ciliates, amoebas, diatoms, dinoflagellates, prymnesiophytes, picophytoplankton

Fungi

Osomotrophs

Viruses (non-cellular)

Replicate in host cell by assembly of pre-formed parts

Phylogenetic tree

A phylogenetic tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities

Based upon similarities and differences in their physical or genetic characteristics

Developed from Darwin’s ideas by Ernst Haeckel

CategorIes through the years

Three domains of life

Previous systems of classification (e.g. Aristotle, Linnaeus, Haeckel, Whittaker et al.) depended on comparison of morphology and physiology

Phylogenetic systems of classification depend on comparison of the information content of their macromolecules – especially nucleic acids and proteins.

Carl Woese (1970s) pioneered the use of ribosomal RNA (rRNA) sequencing and devised the concept of three domains of life

16S ribosomal RNA and its encoding gene

Found in all bacteria andarchaea, eukaryotes have in chloroplasts and mitochondria

Different regions have different levels of variability, ranging from highly conserved to highly variable

Both types of region are essential;

Conserved used to target the gene

Variable used to distinguish between groups

Phylogenies from 16S rRNA genes agree with other genes and therefore represent evolutionary history of the organism

Endosymbiotic theory

Supporting evidence

Organelles have a small genome that encodes some proteins for respiratory chain (mitochondria) or photosynthetic apparatus (chloroplast).

Eukaryotic cells are genetic chimeras, containing DNA from two partners (or more in some cases)

Phylogenetic studies using rRNA gene-sequencing indicate that:

Alphaproteobacteria are the ancestors of mitochondria

Cyanobacteria are the ancestors of chloroplasts

Secondary endosymbiosis led to increasing diversification of eukaryotes

Complexities

Russian nesting dolls

Asgard Archaea - our ancestor?

Possibly the original host

Lokiarcheaum; a member of the Asgard

Two or three domains?

Possible idea for two: TACK Archaea and Asgard Archaea

06 February 2025: Microbial Diversity II

Stramenopiles

General information

’Well known’ algae

Micro (ex. diatoms)

Macro (ex. kelps)

Large diversity

Some are phagotrophic

Includes some important parasites (ex. oomycetes)

Some abundant taxa not well characterised or cultured

MAST (Marine Stramenopiles)

Diatoms

Highly diverse = over 10000 current species and highly varied morphology

Highly important in marine productivity, esp. in temperate and polar regions

Enclosed within a hard silica (SiO2) ’shell like’ structure called frustule

Phaeophytes (brown algae)

Oomycetes

Haptista

General information

Two major lineages

Haptophytes

Haptophytes are the major marine group, mainly photosynthetic, bloom-forming

Centrohelids

Centrohelids mainly freshwater, distinctive radiating pseudopodia

Haptophytes (Prymnesiophytes)

Major members of the phytoplankton, with big influences on oceanic and atmospheric processes

Flagellated unicells in one stage of the life cycle

Often covered with external scales or plates called coccoliths made of calcium carbonate - complex architecture and variety of shapes

Archaeplastids

General information

Contain primary plastid from endosymbiosis with a cyanobacterium

Green algae

All land plants!

Red algae

Glaucophytes

‘Cyanoplasts', or 'cyanelles’ - contain peptidoglycan, possible relic of the endosymbiotic cyanobacteria

Alveolates

General information

Three major groups

Ciliates

Dinoflagellates

Aplicomplexans

Some other minor groups

ex. Perkinsids

Includes some important parasites

Ciliates

Possess cilia in at least one stage of the life cycle – same basic structure as flagellum but cover the cell or are arranged in groups

Synchronous beating creates water currents to channel particulate food into the cell

Over 8000 species, usually 15-80 μm

Major role in microbial loop – ingest smaller flagellates and bacteria (phagotrophic), but are large enough to be eaten by larger protists and mesozooplankton

Abundant in water column sediments and microbial mats

Dinoflagellates

Heterotrophic thecate dinoflagellates cannot increase in volume so are unable to ingest large prey items directly

They extend a pseudopodial “feeding veil” (pallium) with which they surround large prey and secrete digestive enzymes extracellularly

Aplicomplexans

Unicellular eukaryotes that are obligate parasites of other eukaryotes (including animals)

Ex. Plasmodium

Rhizarians

General information

Wide diversity of amoeboid protists

Some major groups include:

Formaminiferans

Acanthareans

Formaminiferans

Shell like organisms

Acanthareans

Ex. Radiolara

Opisthokonts

General information

Unicellular and multicellular groups

Includes protist group

Ex. Choanoflagellates

Animals

Fungi

Defined by a single posterior flagella at some life stage

Choanoflagellates

A single flagellum draws water current through a collar of 30-40 tentacle like filaments – bacteria are trapped and taken into food vacuoles

Fungi

Fungi are an ancient and diverse group of organisms that exist across a wide range of habitats and cell types

Some fungi produce large visible structures, such as mushrooms and lichens, however many fungi are microscopic and, as a result, often overlooked

Chytridiomycota (chytrids)

General information

Retain characters of the last common ancestor with animals

Unicellular body with a cell wall that matures into a sporangium

Within the sporangium, develop uniflagellate zoospores (posterior)

Zoospores swim free to new attachment site and develop into a new sporangium

Most live outside the growth substrate and produce rhizoids that penetrate

Two main trophic modes;

Parasites

Saprotrophs

To understand the ecological and evolutionary importance of chytrids, it is necessary to characterise their life cycle

Chytrid spores (zoospores) have a single ‘tail’ called a flagellum that they use to swim

Once the swimming spores find a suitable substrate or host, they attach and progress through subsequent lifenstages (germling > immature thallus >nmature sporangium) until the next generation of spores is produced

Usually kills the host (ex. frogs)

Chytrids infecting arctic diatoms

Landfast sea ice communities

Barrow, Alaska

Chytrids and the Mycoloop

Chytrids can use substrates not available to zooplankton (too big, inedible)

Chytrid zoospores contain lipid globule, which are readily grazed on by zooplankton

The Dikarya

General information

General trend of increase in ‘complexity’

Broad range of ecological roles;

Symbioses

Parasites

Pathogens

Saprotrophs

Lichens

Lichen microbiomes – symbiosis

Fungi plus cyanobacteria and/or algae

Previously, one cyanobacteria in the symbiosis: Rivularia

We discovered that there are two cyanobionts in the symbiosis:

Rivularia (Nostocales)

Pleurocapsa (Pleurocapsales)

Lichina pygmaea – a marine cyanolichen

Domination of alphaproteobacteria, bacteroidia and cyanobacteria

Gammaproteobacteria at one site (Rame Head)

07 February 2025: Microbial Diversity III

An overview of bacterial phyla

The Bacteria

Bacteria are named and classified by the Bacteriological Code (International Committee on Systematics of Prokaryotes)

Using whole genome phylogeny, there are currently 92 named major divisions (Phyla)

Not all phyla contain organisms that have been cultured; the majority are known only from direct analysis of environmental DNA

The phylogenetic classification of Bacteria is in continual flux – molecular methods often show that organisms grouped on the basis of shared major properties may not be closely related

Linnaean binomial taxonomy

Species: Vibrio coralliilyticus

L. n. corallium coral; Gr. adj. lytikos dissolving; N.L. adj. coralliilyticus coral-dissolving)

Genus: Vibrio

L. v. vibro, to set in tremulous motion, move to and fro, vibrate

Family: Vibrionaceae

Order: Vibrionales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Domain: Bacteria

What is a bacterial species?

In plants and animals, morphological differences, sexual reproduction and geographic separation can be used to explain the concept of species

A group of individuals that can produce breed to produce fertile offspring and are reproductively isolated from other species

This is meaningless for Bacteria

Bacteria are named and identified using a combination of phenotypic, genotypic and phylogenetic properties. Bacteria can be considered of the same species if:

(1) They have more than 70% DNA-DNA hybridization

(2) Their 16SrRNA gene sequences are more than 97% similar

(3) They share a high degree of similarity, with characteristics that distinguish them from other species

Two heterotrophic strategies in ocean bacteria

Most planktonic Bacteria are oligotrophs

Metabolically active, but small size and slow growth rates

Genetically programmed adaptation to low nutrients

Mostly uncultured

Particle-associated copiotrophs have a ‘feast or famine’ lifestyle

Induction of rapid growth rates and large cell size in rich media

Size reduction and other adaptations in response to nutrient limitation

Varying bacterial species

The rosebacter clade (alphaproteobacteria)

One of the most abundant components of coastal and ocean bacterioplankton (>30% of 16S rRNA types)

Carry out anoxygenic photosynthesis

Grow aerobically, but do not produce O2

Close association with blooms of algae and plays a major role in biogeochemical cycles ex. breakdown of DMSP, DMS

SAR11 - Pelagibacter ubique (alphaproteobacteria)

SAR11 clade dominates ocean surface bacterioplankton communities – 25% of all pelagic microbes and up to half of cells intemperate surface waters

Known from 16S rRNA studies since 1990; finally cultured in 2002

Candidatus “Pelagibacter ubique”

Tiny cells – 0.4-0.9 x 0.1-0.2 μm; cell volume only 0.01 μm3

The smallest free-living cell known

Heterotroph

Metabolism of DOM includingC1 compounds like DMS

Cyanobacteria

Synechococus – found mainly in top 20 m in nearly all surface waters

Prochlorococcus - 105 - 106 per ml >25 <200 m (mainly 40oN - 40oS), possess specific pigments to harvest blue light

Different ecotypes at different depths have major differences in genome sequences

Together, these are now known to account for 15-40% of global CO2 fixation and O2 production

Trichodesmium is the most prominent nitrogen fixer in tropical and subtropical oceans (50% of surface waters)

Colonies are made up of trichomes of hundreds of cells and blooms may cover >100,00 km2

Crocosphaera is another abundant nitrogen-

fixer

Some small cyanobacteria fix nitrogen in symbiotic partnership with other organisms

Ex. ,arine Lichens

Candidatus Atelocyanobacterium thalassa (UCNY-A) lives in close symbiosis with prymnesiophyte algae

Sulfur-oxidizing bacteria (SOB, thiotrophs)

A wide range of proteobacteria grow using reduced S compounds as energy source.

Aerobic SOB must find the correct balance of O2 and S

Motility to find optimal conditions.

SOB often occur in microbial mats in association with phototrophs

Many are chemolithotrophic, but some cannot fix CO2 and use organic compounds

Some anaerobic SOB use nitrate as their electron acceptor

These inhabit anaerobic sediments beneath anoxic zones

Ex. off Peru and Namibia where upwelling creates nitrate rich upper layers

Dense blooms of Thioploca form giant sheathed filaments to pick up nitrate, then glide down into sediments to oxidize sulfide

Thiomargarita are giant cells up to 750 μm diameter

Nitrate is stored in the large vacuole and sulfur stored in granules as nutrient reservoirs

The Vibrionaceae family (“The Vibiros”) (Gammaproteobacteria)

Vibrios are typically curved rods with polar flagella

Worldwide distribution in coastal and ocean water and sediments

Major genera

Vibrio, Photobacteroium, Aliivibrio

Commonly associated with the surfaces of marine animals, algae and suspended organic matter

Bioluminscent vibrios

Bobtail squid, anglerfish, flashlight fish

Especially important in the initial colonization of surfaces and biofilms

Includes major pathogens and symbionts

Psychroiezophillic oceanospirillales degrade complex organic compounds

Osedax worms on whale skeletons contain large numbers of intracellular symbiotic Oceanoaspirillales that degrade collagen, cholesterol and lipids from bones

Obligate oil-degrading marine bacteria

Obligate hydrocarbonoclastic bacteria (OHCB)

Alcanivorax

Marinobacter

Thallassolituus

Cycloclasticus

Oleispira

R-strageists

Alcanivorax in the effluent from a column packed with oiled gravel and applied with slow-release fertilizers

Propagation of Cycloclasticus on the surfaces of oil-polluted grains of gravel.

The number of Cycloclasticus cells was estimated by Q-PCR

Crenarchaeota

Since late ’90s, abundant mesophilic and psychrophilic Crenarchaeota were discovered in all the world’s oceans

Methanogens

Production of methane (methanogenesis) is only found among a few members of the Euryarchaeota

Mesophilic or thermophilic obligate anaerobes

These methanogens show high physiological diversity

Methane is ca. 21 x more potent than CO2 as greenhouse gas

Huge reservoirs of frozen methane hydrate under the deep ocean

Evidence of past dramatic climate change due to methane release (55 million years ago, warming by 5-7°C)

Viral lysis is a catalyst of nutrient cycling

Leads to increased bacterial production and respiration

Released DOM is diverted to a closed cycle of uptake and release, whereas protist grazing leads to higher trophic levels in food web

Contributes to release of polymers → micro -scale heterogeneity of seawater

Hydrothermal vent species

Giant Riftia tube worms

Contain large numbers of symbiotic bacteria

Metagenomic studies show these have features of free-living bacteria related to Thiobacillus

Vent chimneys

Covered with huge numbers of Rimicaris shrimp grazing on mats of SOB chimney walls.

They also ‘farm’ episymbionts in a unique gill chamber

Yeti crabs are covered with episymbiotic SOB that are their main source of food