microbial diversity 3

Question 1

bacteria - phyla

Answer 1

currently 92 named phyla ( major divisions )

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

Question 2

bacterial species

Answer 2

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

(1) they have more than 70% DNA-DNA hybridisation
(2) their 16SrRNA gene sequences are more than 97%
similar
(3) the share a high degree of similarity, with
characteristics that distinguish them for other
species

Question 3

heterotrophic

Answer 3

organism that eats other plants or animals for energy and nutrients

Question 4

ocean bacteria : heterotrophic strategies

Answer 4

most planktonic bacteria are oligotrophs:

• metabolically active, but small size and 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

Question 5

oligotrophs

Answer 5

an organism that thrives in an environment that offers very low levels of nutrients

Question 6

copiotrophs

Answer 6

an organism found in environments rich in nutrients, particularly carbon

Question 7

the roseobacter clade

alphaproteobacteria

Answer 7

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 e.g. breakdown of DMSP, DMA

Question 8

SAR11 - pelagibacter ubique

heterotrophic alphaproteobacteria

Answer 8

SAR11 clade dominates ocean surface communities - 25% of all pelagic microbes and up to half of cells in temperate surface waters

known from 16S rRNA studies since 1990 - finally cultured in 2001 - candidatus ‘pelagibacter ubique’

tiny cells : 0.4-0.9 x 0.1-0.2 2 µm; cell volume
only 0.01 µm3

the smallest free-living cell known

heterotroph - metabolism of DOM including C1 compounds like DMS

Question 9

dimethylsulfide (DMS)

Answer 9

a sweet smelling sulfur gas found globally in the upper surface ocean

Question 10

cyanobacteria

Answer 10

• synechococus : found mainly in top 20m in nearly all
  surface waters
• prochlorococcus : 10^5 - 10^6 per ml > 25m < 200m
  ( mainly 40 N - 40 S ) , possess specific pigments to
  harvest blue light
• different ecotypes at different depths have major
  differences in genome sequences
• together they 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 >10000km2
• crocosphaera is another abundant nitrogen-fixer
• some small cyanobacteria such as calothrix fix
  nitrogen in symbiotic partnership with other
  organism e.g marine lichens
• candidatus atelocyanobacteria thalassa (UCNY-A)
  lives in close symbiosis with prymnesiophyte

Question 11

sulfur-oxidising bacteria (SOB, thiotrophs)

Answer 11

• 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 can’t fix CO2
  and use organic compounds

Question 12

chemolithotroph

Answer 12

an organism that is able to use inorganic reduced compounds as a source of energy

Question 13

SOB : using nitrate as electron acceptor

Answer 13

they inhibit anaerobic sediments beneath anoxic zones

dense blooms of thioploca formgiant sheathed filaments to pick up nitrate, then glide down the 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

Question 14

the vibrionaceae family

gammaproteobacteria

Answer 14

worldwide distribution in coastal and ocean water and sediments

major genera: vibrio, photobacterium, aliivibrio

commonly associated with the surfaces of marine mammals, algae and suspended organic matter

especially important in the initial colonization of surfaces and biofilms

includes major pathogens and symbionts

Question 15

bioluminescent vibrios

Answer 15

uncultured vibrionaceae in anglerfish and flashlight fish

vibrio ( aliivibrio ) fischeri in bobtail squid

Question 16

oil-degrading marine bacteria

Answer 16

very specific adaptations

bacteria form a biofilm around the oil droplet and they degrade the oil

obligate hydrocarbonoclastic bacteria (OHCB)

• alcanivorax
• marinobacter
• thallassolituus
• cycloclasticus
• oleispira

Question 17

r-strategist

Answer 17

species whose populations are governed by their biotic potential (maximum reproductive capacity, r

Question 18

the methanogens

Answer 18

member of the archaea domain

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

genus - optimum temp ( degrees )
methanococcus - 35-40
methanothermococcus - 60-65
methanopyrus - 98 (max 110)

Question 19

importance of methane production and utilization in sediments

Answer 19

methane is 21x more potent that 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 year bp - warming by 5-7%)

Question 20

viral lysis is a catalyst of nutrient cycling

Answer 20

leads to increases bacterial reproduction and respiration

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

contributes to release of polymers - micro-scale heterogeneity of seawater