microbial ecology final

overstimulation of mercury

-electricity and heat production, transportation, industry, etc release CO2 emissions -huge mercury output increase following industrialization (prior to this mercury was mostly natural output) -human exposure to mercury through eating fish -human illness such as neurological development, muscular atrophy, etc -convulsions, paralysis, unsuccessful births in wildlife

microbiome

a community of microbes and the environment that they occupy (ex:vaginal bacteria plus epithelial cells, tissue, immune cells, etc)

microbiota

a community of microbes that occupy a specific site or habitat; refer to only the microorganisms not the full environment

soil

a complex mixture of inorganic particles, derived from weathered rock, detritus, and living organisms -divided into mineral soil vs. organic soil -average 40% inorganic matter, 50% air and water, 5% organic matter, 5% living organisms -most microbial growth takes place on the surface of soil particles; soils are most species-rich habitat

competition

a relationship in which different individuals or populations attempt to use the same limited resource (bacteria vs. fungi example)

amensalism

a relationship in which one organism is harmed and the other is unaffected -Produce antibiotics and other toxics that interfere with signaling - block receptors, alter adhesins, quorum sensing interference, degrade signal, degrade receptor, secrete false signal -Alter redox or other environmental conditions (accumulate toxic metabolic end products)

oligotroph

an organism that grows best at very low nutrient concentrations ex: "pelagibacter" most abundant marine heterotroph (in pelagic-open ocean)

pelagic archaea and bacteria

at surface: 10% archaea, 80% bacteria (bacteria dominate at surface waters)) -slowly merge composition percentage -microbial life decreases density with depth at deep subsurface: 45% archaea, 45% bacteria (bacteria and archaea nearly equal in deep waters)

crown galls (parasitism)

crown galls are plant tumors induced by "agrobacteria" with the Ti (tumor induction) plasmid -to initiate tumor formation, agrobacteria cells attach to the wound site on the plant -attached cells transfer a portion of the Ti plasmid to the plant cells *the Ti plasmid serves as the basis vector for genetically engineering plants

detritus

dead organic matter

Arid soils

"desert soil" -when undisturbed tend to form microbial crusts between vascular plants -occurs on 35% terrestrial surface of earth

Metal immobilization

heavy metals are immobilized by improper waste disposal -177 huge underground tanks of failing nuclear waste -leaking waste enters groundwater *major concern is groundwater flow into the Columbia River (flows back and forth) -addition of ACETATE to fuel metal reduction -many metals become insoluble after being reduced and can be removed from the waste

using insoluble electron acceptors

insoluble electron acceptors: how do you get electrons to it if it can't diffuse to them? 1. direct contact 2. electron shuttles 3. nanowires 4. living in filaments with conductive wire

Holobiont

one unit of functional organisms (a host plus all associated microorganisms as one entity for evolutionary selection!) -these organisms hold long-term physical and symbiotic associations -the theory holds that phenotypic variation and therefor natural selection is due largely in part to holobiont's having heritable microbiomes

particle-attached heterotrophic bacteria

pelagic (open sea): <10% bacterial population is particle-attached heterotrophic river/estuary: ~90% bacterial population is particle-attached heterotrophic *cell activity increases by about double when heterotrophic bacteria aggregates

marine water

photic vs. aphotic: hydrothermal vents are especially unique habitat without phototrophs; ~50% of photic zone bacteria have "PR genes" that serve as light-driven proton pumps near-shore vs. open ocean environment: higher nutrients and microbial numbers near-shore compared to open ocean

exploitation

predation, parasitism, disease -one party benefits while the other is harmed

piezophilic

pressure loving, grow best at high atm

organic soils

soil derived from detrital accumulation in bogs/marshes

mineral soils

soil derived from rock weathering and other inorganic materials

piezotolerant

tolerate elevated pressure but grow best at low atm

river environments

typically well mixed organic material- no stratification- due to rapid water flow but susceptible to pollution input -seasons impact light, temperature and flow speed

water distribution

water should remain between 20-50C following treatment to prevent pathogen growth -US safety issues concerned with balancing enough chlorination to kill pathogens without too many unintended chlorination byproducts -buildup of chemical contaminants in water+trying to remove them from drinking water tightens the urban water cycle

methane hydrates

(one of earth's carbon reservoirs) -have the ability to absorb and release methane -form when high levels of methane are under high pressure and low temp (deep sea) -methane (and therefore its carbon atoms) gets trapped underground as methane hydrates -fuel deep sea ecosystems called "cold seeps" -seasonal warming is releasing marine methane hydrates--> a concern!! component of permian extinction anoxia and acidification

acid mine drainage

*all you need is pyrite air and water to start cycle -environmental damage caused by improper handling of coal/minerals rich in sulfides -destroy aquatic communities locally, very expensive to repair, force mines to be abandoned -heavy metals in drinking water

insect-microbe interactions

*genome reduction is a hallmark of obligate insect symbionts -Many relatively unique intercellular mutualisms, a number of hind gut fermentors plus several key "gardening" interactions -Some intercellular mutualisms are required for insect reproduction (splits primary and secondary symbionts)

viral interactions

-"nanoflagellates" and viruses have 5X to 300X the abundance of soil microoganisms -viruses can infect microorganisms in the soil affect soil microbial functioning. -can have positive or negative effects -can contribute to recycling of nutrients within soil microbial populations and mediation of horizontal gene transfer facilitating the responses of microbial populations to environmental changes -parasitism and predation are significant to bacterial mortality **viral abundance is directly correlated to bacterial abundance (ingestion rate depends on prey density) **viruses mediate carbon flow in food chains

hydrothermal vents

-2 types: warm and diffuse or very hot -thermophiles and hyperthermophiles present *chemolithotrophic bacteria and archaea predominate at vent and utilize inorganic materials from the vents

reef-building coral

-coral forms exploitative symbiotic relationship with phototrophic bacteria and protists -coral skeleton is very efficient at light gathering -phototrophic microbes are obtained horizontally or by ingestion -breakdown between host-microbe exchange leads to coral bleaching (too much bleaching leads to death)-->symbiotic relationship is exploitation -high temperature and light impair CO2 transport to the microbes until they are expelled (some have better tolerance to heat stress though)

Nitrogen cycle

-N2 is most stable form of nitrogen and is a major reservoir but usually unavailable to life -life carries out 4 major nitrogen redox transformations: Nitrification: NH4+ -->NO3- Denitrification: NO3- -->N2 (primary way N2 is made) N2 Fixation: N2+8H -->NH3+H2 Anammox: NO2-+NH3 --> 2 N2 (no redox change.. many organisms can do this) Ammonification: organic N --> NH4+

the human microbiome

-all surfaces the of human are colonized by microorganisms -bacterial abundance increase x1 billion down the gut -microbiomes can differ greatly between individuals; it is the genes of the host not the vessel that matters; host genes are also influenced by the microbiome: bacteria from obese mouse transplanted into healthy mouse led to obesity -gut microbiome also impacts behavior (gut-brain interactions) -an individual hosts around 200 species -gut colonization begins at birth and changes with diet (for example vegans vs. omnivores) -active gut flora is required for proper immune system function -reduced functionality of gut microbiome called "dysbiosis" linked to inflammatory bowel disease (dietary fiber and vitamins critical to maintaining healthy microbiota)

herbivory

-animals that consume only plants, herbivory and foregut fermentation has evolved numerous times within mammals -two digestive plans: foregut vs. hindgut fermentation that allow for greater development of mutualistic relationships with complex microbial communities -all mammals lack ability to digest glycosidic bonds (in cellulose)!! herbivores develop mutualisms with anaerobic microbes that can catabolize these bonds

animals eating microbes (predation)

-beneficial if consumer is small to pick up microbes one at a time -larger organisms must perform "grazing" to collect microbes into bunches especially for biofilms -some organisms perform "filter feeding" which filters out microbes from the seawater -final strategy is to ingest the substrate that the microbes are living on; *digestion by bulk substrate ingesting animals significantly reduces microbial biomass

Carbon cycle

-carbon is cycles through all of earth's major carbon reservoirs: rock/sediment 95%, oceans, methane hydrates, fossil fuels, biosphere -carbon dioxide in the atmosphere is most rapidly transferred carbon reservoir -co2 fixed by photosynthetic plants and marine microbes then returned by respiration and especially microbial decomposition

ruminant animals

-herbivorous foregut fermenters (cows, goats, sheep, dear, antelope) -have a special digestive organ called the "rumen" that houses a specialized community of microbes (bacteria, archaea, protists, and fungi) to digest cellulose and other plant sugars -microbes hydrolyze cellulose to free glucose monomers then ferment--> create volatile fatty acids(main food source), methane, and CO2 -the rumen microbes get digested themselves for protein and nutrients

fecal contaminated water

-humans can catch a number of deadly disease from drinking water -4.2% global deaths due to unsafe poor water sanitation -1.8 billion people drink from fecal contaminated water source

Sulfur cycle

-hydrogen sulfide (H2S) is major volatile sulfur gas produced by bacteria via sulfate reduction: SO4-2 --> H2S -sulfide (S2-) is toxic to many plants/animals (reacts spontaneously with O2

terrestrial vs. aquatic environments

-measurement of rRNA for biomass shows 1000x more biomass in soil than water -compared to freshwater environments, marine systems are low in nutrients (especially nitrogen, phosphorous, iron), have saline, cooler temp -marine systems much more dependent on microbial primary producers *microbial activities in ocean are major factors of earth's carbon balance (50% of carbon fixed annually in oceans)

Hawaiian bobtail squid

-mutualistic symbiosis between hawaiian bobtail squid and bioluminescent A. fischeri -shortly after hatching, squid sheds mucus from ciliated epithelial tissue where bacterial cells are harvested from the surrounding environment (horizontal transmission) -after aggregating, these cells move together into pores, through ducts, into deep crypts -bioluminescent bacteria emit light controlled by quorum sensing!! that resembles moonlight for squid to hid from predators -the bacteria is supplied with nutrients by the squid in much higher density than in environment

secondary symbionts

-not restricted to bacteriocytes (can also be sheath cells and hemolymph) -not present in all insects -vertical AND horizontal gene transfer (can be acquired from environment) -can invade cells and live extracellularly -can confer ecologically important traits for survival; may reduce or promote insect fitness *host must provide a benefit for services *some secondary symbionts are parasitic or can manipulate host reproduction

attine (leaf-cutter) ants

-perform "gardening" on cellulose-degrading fungi-->exploitation relationship -in some tropical rain forests, consume up to a third of all leaf mass -queen ant collects fungus and surrounding microbiome (including nitrogen-fixing bacteria) then transmits vertically -worker ants develop mutualistic relationship with bacteria to produce toxin that inhibits the fungal parasite

primary symbionts

-restricted to bacteriocytes -present in all individual insects -insect exhibits extreme gene reduction; retain only genes needed for host fitness -vertical gene transfer (parent to child) -insect requires essential amino acid synthesis and nitrogen recycling

mutualisms with sulfide and methane oxidizers

-some invertebrates with small genomes host symbiotic associations with chemosynthetic bacteria (convert inorganic molecules to organic: sulfide and methane oxidizers) -deep-sea environments (hydrothermal vents and gas seeps) host communities fueled by chemolithotrophic microbes that reduce inorganic materials emitting from the vents -vent tube worms (a host) facilitates growth of the bacteria

sponges

-sponges have ability for archaea symbiosis -archaea performs carbon and nitrogen metabolism for the sponge

drinking water treatment

-surface water CAN be used untreated other then disinfection -deep groundwater requires little to no treatment (chlorinate or ozoninate) -river water processed through "Drinking water purification plants" -well water near rivers will require treatment: filtration prior to disinfection *many US purification plants are built on old infrastructure and are beginning to fail

termites

-termites are major consumers of wood; microbes in their gut can decompose glycosidic bonds in cellulose -anaerobic production of glucose followed by fermentation -"exoglucanase" enzymes (GH7 family) produce cellobiose to break down subunits -"endoglucanase" enzymes (GH9 family) separate cellulose into polymers

pelagic viruses

-viruses are the most abundant microorganisms in the oceans (typically 10x that of prokaryotic abundance) -effect most marine microorganisms -some can inhibit PR genes (photic zone proton pumps) -export via predation or sinking **viruses function as modifiers of the microbial loop

factors affecting soil microbial richness

-water -nutrients (C,N,P) -biotic interactions (relationships) -temp, pH -land use -soil type/particle size -spatial isolation **the obvious exception to low organic matter is oil and natural gas fields

earth's fresh water

3% of water on earth is fresh 30% of that in ground water, 70% in glaciers of that ground water, 87% in lakes

the deep sea

>75% of all ocean water is considered "deep sea" -low temperature (2-4C) -high pressure (piezophilic=pressure loving or piezotolerant) -low nutrient levels -absence of light energy= no phototrophy

neutralism

A relationship between two organisms in which neither species benefits or is harmed

commensalism

A relationship between two organisms in which one organism benefits and the other is unaffected

mutualism

A relationship between two species in which both species benefit -cell-to-cell contact/signaling is key (such as autoinducers!) *common mutualism is syntrophy!! (one organism lives off the products of another) syntrophs provide energy to remove their own waste

Calcium cycle

Ca has an oxidation state of +2. -marine phototrophic and heterotrophic microorganisms use Ca2+ to form exoskeleton intercellular Ca2+ -->decomp or excretion dissolved Ca2+ -->calcification CaCO3--> detriment/rock **increasing dissolution of CO2= lower pH= less CaCO3 more HCO3= ocean acidification

macroaggregates

Soil particles joined together to form larger discrete particles of various shapes and sizes, visible to the naked *eye*. *aggregates="biofilms" that attach to organic matter rather than surfaces

microbes role in mercury

HgS --> sulfide oxidation Hg2+ --> METHYLATION: CH3Hg+ -done by anaerobic prokaryotes! *mercury methylation controlled by gene cluster "hgcA" and "hgcB" **aquatic systems with benthic (bottom bacteria) allochtonous (outside) food sources more so than algae to have high mercury levels (more closed systems are less likely to have fish high in mercury)

microaggregates

Intimate association of soil particles, often clay-*humus*, not visible to the naked eye. *aggregates="biofilms" that attach to organic matter rather than surfaces

Iron cycle

Iron exists naturally in two oxidation states: Ferrous (Fe2+) *stable at acid pH -->oxidation Ferric (Fe3+) -->reduction back to Fe2+ -the redox reactions in the iron cycle include both biological and chemical oxidations and reductions

Manganese cycle

Manganese exists mainly in two oxidation states: Mn2+ -->oxidation Mn4+ -->reduction back to Mn2+ -he redox reactions in the manganese cycle include both biological and chemical oxidations and reductions, although the chemical oxidation occurs much more slowly than for Fe2+ and no know organism has been shown to capture energy from this reaction

soil horizons (top to bottom)

O horizon: un-decomposed plants A horizon: "top soil" dark soil high in organic matter, large numbers of living microorganisms, active microbial activity B horizon: "subsoil" low in organic matter (a lot of minerals/inorganic), lower but detectable microbial activity C horizon: "soil base" develops directly from underlying bedrock, microbial activity very low D horizon: solid bedrock

Phosphorous cycle

Phosphorus exists mainly as P5+. -Main role of microbes is dissolution of insoluble P or decomposition from insoluble compounds P5+ -->decomposition> PO3- --> precipitation makes P insoluble and stored in rocks -phosphorous cycle is dominated by solution/dissolution events and biological recycling - slowest of all the elemental cycles -largest biologically available pools are the oceans and soils Mined for fertilizer (treated with strong acid to make available)

Silicon cycle

Si has oxidation states of -4, +2 and +4 -marine phototrophic and heterotrophic microorganisms use Si4+ to form exoskeletons -very commonly available in oceans (second most common to oxygen)

stratification of deep lakes

deep lakes with high organic input shows stratification; sediments easily become methanogenic

serpentinization

electron donor generates H2 energy for chemolithotrophs in the deep subsurface environment

the deep subsurface

environment in deep soils or fractured rock that is difficult to sample -suitable environment for microbial life with permissive temperature and water presence -4km is max depth for life -groundwater carries organic matter for chemoorganotrophy -deeper you go, more important chemolithoautotrophy (mantle driven gases!)

biogeochemical cycles

life interacts with elements that possess multiple stable valence states with complex redox cycles

lotic

moving freshwater -creek, brook, spring, river, channel, stream

mycorrhizae (mutualism)

mutualistic relationship between plant roots and fungi (as old as land plants themselves) *plant growth is much better with mycorrhizae two classes: ectomycorrhizae- fungal cells form an extensive sheath around the outside of the root with little penetration to the root tissue (primarily in forest trees) endomycorrhizae- fungal mycelium becomes deeply embedded within the root tissue forming "arbuscules"

legume root nodules (mutualism)

mutualistic relationship: legumes and nitrogen-fixing bacteria "Rhizobia" -Rhizobia contain a genetic island that codes for nitrogen fixation and symbiosis; can grown in soil and affect legume plant roots -root secretes signal for bacteria to recognize and bind onto root hairs -invade and travel to the main root -"root modules" form that fix nitrogen -roots supply a controlled level of oxygen to the bacteria to generate energy for nitrogen fixation but not too much to inactivate nitrogenases -significantly increases nitrogen in soil

waste water treatment

primary (50-60% reduction in solids) -screening -sedimentation secondary (85% reduction in solids, 80-99% reduction of pathogenic bacteria and viruses) *alternating anaerobic and aerobic treatment decreases nitrogen in effluent stream which is returned to receiving waters -anaerobic digestion of sludge, incinerated, used as fertilizer or buried **goal is to reduce biomass -aerobic oxidation, trickling filter, disinfection, discharged **goal is to convert dissolved organic carbon to usable biomass tertiary (at least 99% reduction) -further processing of waste water near drinking water quality -additional removal of organic matter/suspended solids -treatment to remove phosphorous!! by chemical precipitation -most complete method but too costly

sand filtration

removes particulate matter from water (including dissolved organic chemicals and microorganisms) and allows biofilm formation

mixatrophs

some phototrophs (with chloroplasts) also consume bacteria

lentic

standing freshwater -ditches, seeps, seasonal pools, marshes, ponds, lakes

microbial leaching

the extraction of valuable metals in biomining such as copper from sulfide ores by microbial activities *20% of worlds copper and 5% gold is carried out by microbial leaching -low-grade ore crushed with water/air added (conditions encourage iron and sulfide oxidizing bacteria) -FE2+-->Fe3+ critical to oxidize metals in the ores -mineralized are oxidized and liquid enriched dissolved metals are recovered *since gold is co-deposited with other materials such as arsenic and pyrite, bacteria leaches away these minerals from the gold to extract it