Envir Micro Biology: Module I

Aurerobasidium pullulans

Aurerobasidium pullulans

type of yeast uthe degrades plastics with polyvinyl chloride

Penicilium, Allescheriella, Phlebia

types of molds that degrade hydrocarbons in petroleum and pesticide products

Phanerochaete chrysoporium

fungi that degrades synthetic dyes and plastics, polyaromatic hydrocarbons, benzene homologs (fossil fuels)

slime molds

type of fungi

→ form spores

→ live in decaying organic matter

→ phagocytize bacteria

amoeboid

vegetative cellular state of slime molds

plasmodia

vegetative acellular amorphic protoplasm masses

protozoa

single-celled, saprotrophic or phototropic animals

→ found in FW, marine habits, soil, and animal gastrointestinal tract

→ no cell wall

→ bacterivrours or phagocytoic

→ formation of cysts/oocytes for reproduction

hydrogenosomes

organelle instead of mitochondria found in anaerobic and microaerophilic protozoan

fiber digestion, water contamination

roles of prptozoans in the enviroment

Naegleria, Giardia

protozoans responsible for water contaminations

Algae

single of multicellular protists

photosynthetic

identification based on cell carotenoid properties

endolithic

algae that grows attached to a surface

planktonic

algae that is suspended in the water column

neustonic

algae that is at the air-water interface

pyrenoids

storage and starch synthesis in algae

xanthophylls

algal pigments

cellulose

most algae;s cell walls contain this molecule, along with polysachharides

cell wall

cellular structure that is absent in egulenoids

ph <4

algal acidity tolerance

bacteriophages

viruses that infect bacteria

mycovirsues

viruses that infect cyanobacteria

Coliphages

viruses that infect coliform bacteria

crenarchaeota

phyla of archaea that are thermophiles

Euryarchaeota

phylum of halophile archaea and methanogens

Prions

abnormal proteins can be transferred across species

→ Transmissible spongiform encephalopathy (TSE)

→ transformation of alpha helixes to beta sheets

→ PrPsc: Infectious upon contact

peds

inorganic aggregate formation enhanced by organic microbial gums/slimes

→ held together by polysaccharides metabolites

→ additionally binding from fungal hyphae/plant roots

→ more clay; intact

→ less less: fragile

Intraaggregates pores

pore spcaes within a secondary aggregate

interaggragte pores

spaces between secondary aggregates

→ can be increased by plant roots, worms, animal interactions

→ water travels slower with small pores (micropore exlusion). Smaller pores occur in silt and clay particles(less coarse soil)

Surface soil

weathered end product of climate and living organisms on soil parent material with a particular topography

unsaturated

Vandose Zone

Zone of soil that is unsaturated, oligotrophic subsurface

→ mostly unweathered parent material

→ thick layers: less microbial activity due to oligotrophic enviroment

→ low organic carbon content (<1%)

→ no spontaneous water movement

Remediation zone

Vadose zone serves as this to avoid groundwater contamination by a remedial foam agent

Shallow Table Aquifers

Apart of the saturated zone

→ Highest organic carbon content

→ mostly connected to Earth’s surface

→ obtain water from rainfall

→ active rapid groundwater flows

→ Aerboic enviroment

Saturated zone

→ oligotrophic parent material

→ saturated with water

→ porous

→ 3 types in form of aquifers: shallow table, intermediate, and deep aquifers

Capillary fringe

boundary between vadose and saturated zones that changes from rainfall levels

Intermediate Aquifers

→ type of saturated zones

→ slower flow rates

→ provides a portion of irrigation and drinking water

Deep Aquifers

→ apart of the saturated zones

→ lowest lying aquifer

→ anaerobic environment

→ slow flow rates

Wetlands

areas where the water table is at or above Earth’s surface

mostly seen in temperate climates

→ Swamps, bogs, marshes

Sphagnum

mosses that dominate bog wetlands, can adsorpb cations from water well, resulting in the release of H+ ions and in exhnage increase the acidity of soil

Peat

collection of dead plant material found in bogs, which occur due to the completel submergence of plant material in waterr, which limits dissolved oxygen and slows decompostion

Bog

type of wetland with an anaerobic and acidic environment, characterized by slow decomposition rates. Low water flow

Solid Phase

phase of the soil that are influcence by particle tectures, soil architecture, soil pH, CEC, soil profiles

sand<silt<clay

primary particles in soil

Silicon, Oxygen

Abundant minerals in soils

clay

soil that is has well-defined peds, intact contains a high percetange of which particle

O Horizon

dark, organic rich layer of soil

A Horzion

light layer with accumulation of humidified organic matter

E Horzion

invovled in eluviation of the A Horzion

Eluvation

removal/transport of nutrients/inorganics from A Horizon

Illuviation

deposition of substances

B Horizon

profile that illuviation E horizon substances into itself

C Horizon

soil profile of unweathered parent material,transition between soil and vadose zone

R Horizon

Bedrock

pore space

pores (intra or inter-aggregates) within the soil structure.

micropore exlcusion

phenomenon where water travels slower with small pore spaces

Cation Exchange Capacity

primary mechanism of sorption(organic/inorganic associations with solid phase)

→ the amount of nutrients that can be stored and released in plants

→ determined by cation concentration and the affinity the soil has for adsorption

→ positively charged cations adsorb to negative clay particle surface

coarser

a soil with a higher sand content will be,

finer

soil with a higher silt/clay content

Exchange Sites

cation sites that are more electronegative and high surface area

→ higher charged, smaller cations have a higher affinity for cation exchange site(3+ and smaller cations like to hold onto electrons from ions)

Electrical doubler layer

layer of positive counterions that adsorps microbes to clay via a divalent cation

acidic soils

high rainfall → loss of cations via cation leeching →

alkaline

more water evap→ salt acculation→

Organic Matter

layer of soil that is 1-5% surface soil, <.1% below surface soil

→ live biomass

→ humic substances (heterogenous polymers formed from dead/decaying biomass)

Humus

layer of spongelike organic material

in the O Horizon

contains carboxyl and phenolic hydroxyl groups, used in CEC

Hydrophobic filaments sorb nonpolar solutes from soil(hydrophobic binding)

provides carbon and energy for microbes

Liquid Phase

the phase of soil characterized by the organic and inorganic solutes in an aqueous solution

→ control the amount of microbial and plant growth

→ microbes surrounded by a water film for nutrient uptake/waste disposal

soil Water potential

the work per unit quantity necessary to transfer an infinitesimal amount from a specific elevation and pressure to another point somewhere else in the porous medium

→ high to low movement

Matric/Capillary forces

attraction of water into soil pores(adhesion and cohesion) force that forms the second layer after adding water to the system

→ contributes to the rise of free water from the water table

→ primary action in unsaturated soils

→ greatest in force when running through soils with small pores

Surface forces

helps compact the nearly immobile water film layer

gravitational force

force that exerts a positive force down which is being held in the pore space

Field Capacity

point in soil that is moist, ut drained that is in optimal conditions for aerobic microbes

oxygen

key element that allows for aerobic degradation of organic matter in the soil atmosphere

Allopathic secretations

response to biotic competition stressors

inhibitory/toxic substances released that harm neighboring organisms

ex: Penicillin

Predation/Parasistism

biotic stressor competition for microbes

grazing on bacteria or infecting plants

6-8

pH tolerance for microbes

redox potential

depleted oxygen lowers this, not good for microbes that use O2 for respiration

→ decreases with depth

Mesophiles

microbes with temp toleration of 20-45 C

Thermophilic

microbes with temp tolerance of 20-45C

Psychrophiles

microbes with temp tolerance <20C

dominate, dry soils

type of soil that actinomycetes compete in

low-pH

type of soil that fungi dominate in

>8

competitive pH of Actinomycetes

<5

competitive pH of fungi

Mehanogensis

archae play a key roll in this process

synthesis of methane → into atm → fixed into Co2

carbonic acid

algae perform this that is like weathering in soils

exopolysaccharides

secretions by fungi that glue clay particles into micro aggregates

Teichoic Acids

polymers of glycerol or ribitol joined by phosphate groups that extend from the surface of a GRAM POSITIVE cell

→ antigenic

→ helps mediate cell interactions

Lipopolysacchardies

imuunogenic and endotoxic protection in GRAM NEGATIVE bacteria

O antigen

side chain resposnbile for hyperallegenic reaction in lipopolysaccharide

conidia

asexual spores of fungi

Plasmodia

amorphic protoplasm masses of slime molds

aersols

particles suspended in air

→ smaller particles can travel further and stay suspended longer

PM10

aersols < 10 micrometers

PM2.5

aersols <2.5microm

nuceli mode

aersol <.1 microm(fine particle)

accumulation mode

.1-2 microm (fine particle)

coarse mode

> 2 microm(coarse particles)

→ most protozoa, fungi and bacteria

Point Source

PHASE 1: LAUNCHING

bilateral is spread through an isolated and well-defined point

→ conical dispersion (instantaneous or continious)

Linear and Area Source

PHAE 1: LAUNCHING

bioaerosol launched through wave dispersion. Occurs over a less well defined area

→ ex: plane aerosols, cropland, animal activity

Submicroscale transport

PHASE II: TRANSPORT

bioaersol moves in short periods of time (<10 min) and distance (<100m)

→ ex: within buildings, confied spaces

MIcroscale Transport

PHASE II: TRANSPORT

bioaersol van transprot for 10min - 1 hr, in distances from 100m to 1 km

Mesoscale Transport

PHASE II: TRANSPORT

bioaerosol can travel up to 100 km