1

Microbiology in the News Jan th

14 , 2017
Superbug Resistant to Every Antibiotic in the U.S. Killed Nevada
Woman
A CDC report concludes that the woman, who died last August,
succumbed to a Klebsiella pneumoniae infection that was resistant
to 26 different antibiotics.
70 year old woman broke her femur and was treated in India 2 years prior died in
August/September
CRE carbapenem resistant bacteria (enterobacteriacea)
Last resort antibiotic, Colistin, was ineffective

Will this antibiotic resistance kill 10 million people by 2050? (CDC

reports)
Depressed? Go play in the dirt.
As effective as antidepressants
Mycobacterium vaccae worked in mice
Increased vitality and cognitive function,
decreased pain in cancer patients
Stimulates immune system via
cytokines
Stimulates serotonin production
Elevates mood and lessens anxiety

A healthy immune system is important

for maintaining mental health

So play in the dirt!

4
 What bacteria makes earthy smell?

Streptomyces (Actinomycetes) produces terpenes geosmin and methylisoborneol

About 37 million friends are joining you every hour.

~ 18% from humans

Cell phone outline bacteria cultured from phone
 Microbiology
Microbiology:
The study of living things too small to be seen without magnification

Microbiology revolves around two themes:

1. Understanding basic life processes

2. Applying that knowledge to the benefit of humans

Microbes play important roles in medicine, agriculture, and industry

Only a small minority of microorganisms cause disease. Many more are useful or
essential for human life

Genetic and physiological diversity of microbial life exceeds that of plants and animals

Microorganisms affect and support all other forms of life

Planet of the Bacteria
Bacteria are at the center of maximal influence and importance of life on this
planet

Oldest form of life

Fossil records 3.5 billion years ago preceded 1st animals by 3 billion years
Ubiquitous
can live in places unsuitable for other organisms
40 miles up, 7 miles deep

Largest mass of living material on Earth

The normal flora found on our human bodies contains 10X more bacterial cells than cells of our body
5 x 1030 bacteria in the world

Carry out major processes for biogeochemical cycles

Microbial life has shaped our atmosphere, our geology, and energy cycles of all ecosystems

Other life forms require microbes to survive

Oldest Form of Life on Earth

11
 Words oldest fossils found in Pilbara
Jan 1, 2013
Martin Brasier, Oxford University, David Wacey ,U of Western Australia
Western Australian rocks hold
fossil record of bacteria that
lived 3.49 billion years ago
What about Archaea?
Only found as textures of mats
of bacteria on surfaces of
sandstone (stromatolites)
Sulfur-based networks of
collective behavior

NASAs Curiosity rover is

equipped with instruments able 3.4 bya
to detect similar fossils
UPDATE! UPDATE! August 2016
Oldest fossils on Earth discovered in 3.7bn-
year-old Greenland rocks
Stromatolites in rocks of Isua suprcrustal belt
in SW Greenland
4.2bya, oldest known rocks

Stromatolites 220 million years older than

previously discovered

Does this raise questions about the

possibility of life on other planets?
Because, If we have have life at 3,700
million (3.7 bn) years on Earth, did it exist
on other planets
because Mars, for example, 3,700 million
years ago was wet
13
 Pre-Jurassic Park: Ancient, immortal?
In 2000 AD scientists at West Chester University in
Pennsylvania succeeded in waking up the resting spores
of a bacterium (Bacillus permians) that was last active
250 million years ago.

The question this caused scientists to ask was,

Is it possible some Bacteria may be immortal?

Salt crystals from

the Permian Sea
 Melting Glaciers Liberate Ancient Microbes
Revived bacteria encased in 750,000
year old ice.

Suspended animation for a millennia.

Oldest ice on earth 1-8 million years

Also the largest virus ever found

And a 140,000 year old plant virus in
Greenland

Cells and carbon dumped out of

melting glaciers could be a huge
reservoir of decomposing organic
matter generating CO2 and CH4 as
they decay. April 2012
Ubiquitous

16
 Bacteria are ubiquitous
40 miles up, 7 miles deep
bacteria live in all habitats accessible to any
form of life, while the edges of life's toleration
are almost exclusively bacteria

10% of insect guts

400oC black smoker vents

Gills of deep-sea mussels sulfur-oxidizing symbiont
that can also use hydrogen as an energy source
Chemosynthetic bacteria living inside tubeworms
Socompa volcano in the Andes
19,850 water, methane, CO2
Intense UV radiation

pH, temperature, salinity, radiation, oxygen,

pollution
 July 13, 2014 Grimsvotn Lake, Iceland

>400 Subglacial Antarctic Lakes

Lake Grimsvotn, found beneath glaciers
Lake 100 meters deep
Covered by 300 meter ice sheet
Has heat rising from volcano beneath it, so
doesnt freeze
Similar to Martian terrain?

Lake Vostok in Antarctica

Largest subglacial lake

July 21, 2014 Lake Whillans

800 meters below W. Antarctic ice sheet
120,000 1million years since sunlight
reached there
3,931 types of bacteria and Archaea
18
 Antarticas blood red waterfall and ancient
bacteria
Taylor Glacier in the coldest, driest
place on earth empties into Lake
Bonney
The subglacial lake, under a
quarter mile of ice, is so salty it
does not freeze.
Lake has no oxygen, no sunlight
Rich in iron in contact with air it
rusts.
Many bacteria live in the lakes
under the glaciers
17 different autotrophs
Energy obtained from sulfates
Iron interacts with by-products to
restore sulfates
19
Not only that, butbacteria and bioaccumulation of
mercury
Mercury-loving bacteria
An international team of
scientists have found a
bacterium, Nitrospinia, that is
converting mercury to more-
toxic methylmercury on
Antarctic sea ice.
Travel to Anartica through the
atmosphere

20
 Pitch Lake: an earthy hydrocarbon body
Pitch Lake, a lake made of asphalt and
filled with hydrocarbon gases on the
Caribbean island of Trinidad

Microbes live in tiny droplets of water, 50

times smaller than a typical raindrop.

Most abundant material are Burkholderia

Methanotrophs
Halobacterium

Aug 21, 2014

21
Berkeley Pit Lake: Butte, MT
Former open-pit copper mine until 1982
Toxic, acidic water
Copper, iron, arsenic, cadmium, zinc, sulfuric acid
Unique extremophile microscope life forms -
New fungal and bacterial species have
adapted to these harsh conditions
142 species
80 chemical compounds that exist no where else
Bacteria produce highly toxic compounds to
improve their survivability
Some products show selective activity against
cancer cell lines
Breast, ovarian and lung cancer cell lines
22
 Tersicoccus phoenicis.
Thrives in the cleanest places on
Earth where spacecraft are
assembled
Withstands chemical cleaning
Withstands UV rays Discovered in spacecraft clean rooms, one at NASAs Kennedy Space Center, and ESA
Survives a dearth of nutrients spacecraft cleanroom in French Guiana, a European Space Agency facility in South
America. 11/7/2013
 Curiosity may have taken Earth bacteria to
Mars (May 2014)
Bacillus
11% of 377 strains survive NASAs
scrubbing conditions.
UV desication, cold, pH extremes
Not all formed spores used other
biochemical means of protection
Metabolic changes

Contamination of other planets with

earth life forms!
Or, thinking life is discovered..
Biomass

25
 Biomass of Bacteria
Largest mass of living material on earth
5x1030 g
Most of the prokaryotes reside in three
large habitats: seawater, soil, and the
sediment/soil subsurface
1998 first scientific study
40 million / g of soil
1 million / ml of fresh water
5 105 cells/ml ocean
1 107 viruses /ml
Carbon content 5 x 1017 g
> total C found in plants
Largest pool of N and P
350-550,000 tons
 There are more microbes in a teaspoon of soil
than there are people on earth

There are more microbes on earth than stars in

the universe

27
How long would it take E.coli to reach a mass
equivalent to planet earth?
The doubling time for E. coli = 20 minutes

Mass of the E. coli bacterium = 10 -12 g

Mass of the earth =5.9763 x 1024 kg

What is the mass of a colony of E. coli after 1 day (24hrs) of

exponential growth from one single e-coli bacterium?

t=2639 minutes or ~44 Hours or ~ 1.8 days

Thank goodness for that anti-bacterial soap.

28
 Because the number of bacteria is so large, events
that would occur once in 10 billion years in the
laboratory would occur every second in nature.

New species, anyone?

29
Biogeochemical cycles

30
 Biogeochemical Cycles
Bacteria (along with fungi) are the main
reducers of dead organic matter and are
one of the two major links in the
fundamental ecological cycle of production
(photosynthesis) and reduction to useful
forms for renewed production
Closed systems!
Carbon, Nitrogen, and Sulfur

Oxygen started to accumulate in the

atmosphere about 2 billion years ago,
substantially before the evolution of
multicellular plant life
31
 The global nitrogen cycle
All life depends on the
oxidative and
reductive conversions
of nitrogen
most of which are
performed only by
microbes

32
Adapting to Elevated CO2 Sept 2015

High carbon dioxide levels

can irreversibly rev up a
cyanobacteriums ability to
fix nitrogen over the long
term, a study finds.
A key phytoplankton can adapt
metabolically to long-term high carbon
dioxide (CO2) levels, and those adaptive
changes can become permanent
T. erythraeum is widely distributed in the worlds Massive bloom or surface aggregation
oceans and is important to the marine food web of Trichodesmium near New Caledonia in the
because it fixes nitrogen, making the element
available to other organisms in the ocean. tropical Pacific Ocean, as viewed by a satellite
from space
33
 Biogeochemical Cycles
green-stained Pseudomonas syringae, a
Bio-precipitation do bacteria control plant pathogen, is efficient at
weather? nucleating ice and is commonly found
in clouds
Cloudborne bacteria may pose climate
threats by boosting the production of a
greenhouse gas
degrade organic pollutants to carbon
dioxide at least as efficiently as the sun

Ice-nucleating bacteria
hailstones found with concentrations up
to 1,000 cells per milliliter of meltwater
in the cores
biological nuclei can cause freezing at
warmer temperatures
 Bacterias impact on climate Nature, May 16, 2016
Chemoorganotrophic alpha proteobacteria
Pelagibacterales -stimulates cloud formation
Abundant in oceans (1 in 3 bacteria, 500 million per
tsp)
Important for climate stability
produce environmentally important gas, DMS, from
DMSP that is produced by marine plankton
Dimethylsulfide (and methanethiol) from
dimethylsulfonioproionate

CLAW hypothesis
Planets temperature is stabilized through a negative
feedback loop
Sunlight stimulated abundance of phytoplankton
Phytoplankton produce DMSP
DMPS broken down into DMS by other microorganisms
DMS increases cloud droplets
Reduces how much sunlight hits the ocean surface 35
All life depends on microbes

36
Bacteria: Diversity, ubiquity, functional capacity
Strong interdependencies and complex interactions between the domain
Bacteria and complex multicellular organisms
Archaea, fungi, plants, animals
Nutrition, protection

Bacteria play a role in animal biology from development to systems

biology
animal development and physiology, and critical roles in ecological frameworks.
Symbionts are developmental signals, recruited several times in evolution
Origins of multicellularity to drivers of morphological complexity

Bacterial play a role in the very origins of animals

37
 Microbiota

Metabolic activity Molecules as signals

Processing or transfor- Competition against Induction of immunity Induction of other

mation of nutrients, detrimental microbes: maturation and developmental
vitamins, etc. antibiosis immunity modulation transitions

Host nutrition Host protection Host

development
Taken from Trends in
Microbiology
 Human Flora
Microbial fife saturates and infuses the human body
And we cannot live without

10% of our dry body weight

Our bodies contain over 1,000 species of bacteria

Only about 50 are potentially pathogenic
Over 500 species live on human skin
20 million microbial genes in our bodies
1000X more than the 20,00 protein-coding genes in the human
body

The lives of humans and microorganisms are

inextricably linked

Our microbiome is like an extra organ of the human

body but with many functions
How did the associations first evolve?
All development of life originated and evolved in a microbe-rich
environment

Orchestration of ontogeny and interdomain communication.

40
Animals through time

Interactions between bacteria and eukaryotes

Immunity
Multicellularity
epithelia
Gut cavity
Organs
Adaptive Immunity
Development and Metamorphosis: Hydroides
elegans marine tubeworm
Jan 9th, 2014
Settles on hulls of ships
Must transition from free-
swimming larval stage to
anchoring juvenile
Metamorphosis
accomplished by a set of
bacterial genes of
Pseudoalteromonas
luteoviolacea
Make components of
structures resembling
contractile tails of
bacteriophages
42
 The
termite
gut:
shared
evolution

Habitat
Distribution and diversification: 90% of bacterial species in termite guts are not found
elsewhere. The termite gut provides a novel physical environment for bacterial
colonization. 43
Humans create environmental
conditions for novel bacterial
metabolic pathways
Hydrocarbons
PCBs
PAHs
Bacteria remove uranium contamination.
Pharmaceutical
substances
Metals, etc.

Bioremediation and
Biotransfomation
Xenobiotic metabolism 44
Some homologous gene
products provide
signaling between
extant animals and
bacteria

45
 Bacteria have social behaviors:
Communication
Intra species chemical signaling
Quorum sensing
Interspecies signaling
Interdomain communication
From Host
NO
Hormones
Same genomic dictionary of language from the common and deep evolutionary ancestry.

Did communication evolve to maintain a balance and association with beneficial

species and pathogens hijacked the conversations to increase their own fitness
through disease? 46
Signaling within and between the animal and its
microbiota
 Nested ecological interactions
Cascading effects of animal-bacterial
interactions across multiple scales
Bacterial symbionts residing in the gut are
essential to nutritional success of insect
species
Diversity of energy metabolisms in
bacteria and animals.
Animals can ferment and aerobically
respire but cant perform other
ecologically vital energy-harvesting
processes.

Animals are directly or indirectly

dependent on bacteria for extracting
energy and cycling biomolecules.
48
 Hydrothermal vents: Nested Ecological
Interactions
> 350oC
Hydrothermal vent communities illustrate the role of
animal microbe associations in such nested
ecosystems.
At vents and other reducing habitats,
chemoautotrophic symbionts provide organic
nutrients for animal hosts in at least seven different
phyla.
Bacteria keep hydrothermal vents alive

The activities of these individual symbioses

contribute to larger communities that include
nonsymbiotic animal and microbial species that are
able to exist through the symbiotic primary
production that is not driven by solar energy but
rather by sulfide, hydrogen, methane, and other
reduced energy sources
Black smokers and white smokers

courtesy of NOAA 50
Bacteria, Archaea and viruses

This shows a cross-section

view of a thermophile.
Notice all the viruses in the
cell. Viruses are much
smaller than bacteria and
are abundant at deep-sea
vents. Photograph: Terry
Beveridge.

This is a microscopic view of a bacterial

community from a hot spring in the Azores.
None of them have names because none of
them have been identified. Scale bar is 1 m
(1/1000 of a mm). Photograph: Paula Aguilar.
51
 Aphidus ervi
Acyrthosiphon pisum

52
THE MICROBIAL WORLD complex
symbiotic systems

Bacteriophage (mobile genetic element)

APSE I, II (maybe others)
Transmits resistance via toxins
Bacterium
Hamiltonella defensa facultative secondary
symbiont
Buchnera aphidicola - Primary symbiont (lives
w/in specialized cells)

Predator Wasp
Aphidus ervi

Plant-eating insect
Pea aphid Acyrthosiphon pisum
 Behavioral adaptations
How does the parasitoid wasp, A. ervi, counteract the symbiont defense of
the pea aphid, A. pisum?

1. Wasps can transmit the protective bacteria by stabbing an uninfected

aphid after an infected one.
Now are aphids protected?

2. If wasp detects infection with the symbiont, H. defensa, the wasp will lay 2
eggs instead of one.
Can detect infected and uninfected aphids, and selectively superparasitize only
infected aphids

Wasps may detect pheromone alarm of the aphids. If aphids have bacterial
protection, their message is sent out at a reduced level.
54
Many parasitoid wasps lay
their eggs inside a living
insect larva. When a female
wasp deposits her eggs
inside a lepitdopteran
caterpillar, she also deposits
her symbiogenic
polydnavirus virions,
which only express wasp
genes. These genes are
expressed in the caterpillar,
where they prevent the
encapsulation process that
would otherwise wall off and
kill the wasp egg.
2011
The panic grass Dichanthelium lanuginosum is found in geothermal soils in Yellowstone National
Park, USA, where it can grow at soil temperatures >50 C. The plant requires a fungal
endophyte, Curvularia protuberata, to survive at this temperature. In turn, the fungus
requires a virus, Curvularia thermal tolerance virus (CThTV), to confer this thermotolerance
effect.
 Survival of life
Biodiversitys holy grail is the soil
Diversity of trees
Even wine grapes!

All life on Earth is connected in a web

of relationships. Every creature, no
matter how small, has a job to do, and
microbes are the workhorses of the
living world.
Environmental continuum

From climate change to the need for

renewable energy sources, the threat
of new pandemics and the general
demise in environmental quality - the
role of micro-organisms in each of
these challenges is crucially important
 Members of the
Microbial World
Organisms and acellular entities too
small to be clearly seen by the unaided
eye
some < 1 mm, some macroscopic
These organisms are relatively simple in
their construction and lack highly
differentiated cells and distinct tissues

1 10 M most bacteria
Minimum size of a known
microbial cell 0.2 mm
59
60
 Really large bacteria
The largest bacteria ever found Thiomargarita
namibiensis
0.75 1 mm in diameter (visible to the naked eye) 3
million times normal
Sulfur Pearl of Nambia
Large size comes from vacuole that stores nitrate (10,000X)
Nitrogen and sulfur cycle works together
Detoxifiers (eats sulfur)
Cant cultivate outside of natural environment

Epulopiscium fishcelsoni
5-600 mm
Found in guts of surgeonfish, symbiotic
Convoluted membrane to increase surface area
Motile; change pH of hosts gut fluids differentially during
day and night
Has many copies of its genome
Cant cultivate outside of its host
 Really small bacteria
Nanoarchaeum equitans 400 nm:
thermophile,
obligatory symbiont on achaeon Ignicoccus

Nanobes: 1/10th size of smallest bacteria.

Tiny filamental structures

Mycoplasma genitalium smallest organism

capable of independent growth and
reproduction. 200-300nm
Ultramicrobacterium
No cell wall
 Summary
Bacteria are the dominant forms of life on Earth

Earth contains more bacterial organisms than all others combined

Total bacterial biomass exceeds all the rest of life combined (even plants, trees)

Bacteria live in more places and work in a great variety of metabolic ways
Overwhelming number, unparalleled variety

Bacteria alone constitute the first half of lifes history and continue in
diversity to this day
Form the root of lifes entire tree
 Summary
What do microoganisms provide for their hosts?
Nutrition, protection, development
Biogeochemical cycles
Precipitation, carbon, nitrogen and all of them
Biomass
Nested ecological interactions
Aphid, wasp, virus
Acyrthosiphon pisum, Aphidus ervi, Hamiltonella defensa , Buchnera
aphidicola -
APSE I, II
Largest and smallest bacteria
By name
Thiomargarita namibiensis
Micoplasma genitalium 64
 Next-generation sequencing has identified scores of new microorganisms.
Getting even abundant bacterial species to grow in the lab has proven
challenging
nutrients, a carbon source, and time are
usually not enough to coax bacteria isolated
from the wild to grow in a laboratory
setting.
1873, Joseph Lister liquid medium and in 1880 Robert Koch solid
media

What else is needed?

Signaling molecules
Physical signals from neighbors
community
Colored scanning electron micrograph of a segmented
Human microbes easier to culture (>1/2) than filamentous bacterium (SFB, orange) reaching up from a
environmental bacteria (<1%) bed of mouse intestinal cells (green). SFB was successfully
cultured for the first time this year, a half a century after it
Bottleneck of cultivation was first discovered. (October 2015)
65
OTUs
There are about 12,400 cataloged bacteria species according to the List of
Prokaryotic Names with Standing in Nomenclature, and most of these can
be cultured to some extent.

But these represent only a fraction of the presumed millions of species of

microbes in the world, and only about half the known bacterial phyla
have at least one cultured species.

Smarter tools are needed.

Communication among the bacterial community is key

66
 iCHIP - 2010

A multiwell diffusion chamber separates individual bacterial cells in the wells of a 384-well plate. A
breathable membrane surrounding the plate allows interaction with the natural environment, such as soil
or ocean water, and sensing of the multitudes of molecular factors produced by neighboring bacteria 67
iCHIP used to discover new antibiotic
teixobactin (Jan 2015)

68
 Microdroplet-microcolony formation

A device traps individual bacteria inside tiny, permeable gel droplets, which allow interactions among
bacteria while keeping them separate. The droplets are bathed in a nutrient-rich media until a
microcolony of 40200 cells forms inside, then sorted and plated for further analysis. 69
Microbes shape Human history
Yeasts and bacteria made foods
Breads/cheeses
Alcoholic beverages
Mining
Copper, uranium and zinc produced by bacterial leaching

Microbial diseases devastate human populations

TB, leprosy, bubponic plague etc etc

Bioremediation
The management of our planets biosphere (global warming and pollution)
depends on our understanding of microbial ecology
70
 Microorganisms, Energy, and the
Environment.

The role of microbes in biofuels production

For example, methane, ethanol, hydrogen

The role of microbes in cleaning up

pollutants (bioremediation)

Microorganisms and Their Genetic

Resources
Exploitation of microbes for production of
antibiotics, enzymes, and various
chemicals

Genetic engineering of microbes to

generate products of value to humans,
such as insulin (biotechnology)
Impact of Microorganisms on Humans -
agents of disease
 1900 Today
Influenza and Heart disease
pneumonia
Tuberculosis Cancer

Gastroenteritis Stroke

Heart disease Pulmonary

disease
Stroke Accidents

Kidney disease Diabetes

Accidents Alzheimers
disease
Cancer Influenza and
pneumonia
Infant diseases Kidney disease

Septicemia Infectious disease

Diphtheria
Nonmicrobial disease
Suicide

0 100 200 0 100 200

Deaths per 100,000 population Deaths per 100,000 population

Death rates for the leading causes of death in the United States
 2008

Low-income countries Deaths in millions % of deaths

Lower respiratory infections 1.05 11.3%

Diarrhoeal diseases 0.76 8.2%
HIV/AIDS 0.72 7.8%
Ischaemic heart disease 0.57 6.1%
Malaria 0.48 5.2%
Stroke and other cerebrovascular
0.45 4.9%
disease
Tuberculosis 0.40 4.3%
Prematurity and low birth weight 0.30 3.2%
Birth asphyxia and birth trauma 0.27 2.9%
Neonatal infections 0.24 2.6%
 Deaths in
High-income countries millions
% of deaths

Ischaemic heart disease 1.42 15.6%

Stroke and other cerebrovascular disease 0.79 8.7%
Trachea, bronchus, lung cancers 0.54 5.9%
Alzheimer and other dementias 0.37 4.1%
Lower respiratory infections 0.35 3.8%
Chronic obstructive pulmonary disease 0.32 3.5%
Colon and rectum cancers 0.30 3.3%
Diabetes mellitus 0.24 2.6%
Hypertensive heart disease 0.21 2.3%
Breast cancer 0.17 1.9%
 #1

#2

10 most common infectious causes of death world wide

79
80
Deaths attributable to antimicrobial resistance every year by 2050

81
82
84