Ecology

Associations

In Great Britain and/or Ireland:
Bacterial predator
Aplectana is predator of Bacteria

Bacterial predator
Cosmocerca is predator of Bacteria

Bacterial predator
Entamoeba muris is predator of Bacteria

Bacterial predator
larva of Graphidium strigosum is predator of Bacteria

Bacterial predator
larva of Nematospiroides dubius is predator of Bacteria

Bacterial predator
Syphacia obvelata is predator of Bacteria

Bacterial predator
Syphacia stroma is predator of Bacteria

Bacterial predator
larva of Trichostrongylus retortaeformis is predator of Bacteria

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Known predators

bacteria (Benthic bacteria) is prey of:
Streblospio
Capitella
Manayunkia
Littorina
Modiolus
Sesarma
Uca
Chironomidae
protozoa
Rotifera
Nematoda
zooflagellates
ciliates
meroplankton
Appendicularia
Doliolidae
Calanoida
Oligochaeta
macrobenthos
Actinopterygii
Bosmina
Chydorus
Tropocyclops
Copepoda
Tubificidae
Paraplectonema
Limnocythere
Synchaeta
Polyarthra
Conochilus
Daphnia
Eudiaptomus
benthic herbivores
Decapoda
detritivorous invertebrates
detritus
bacterial and fungal feeders
Diptera
Mysidacea
Ostracoda
Euphausiacea
Hyperiidea
Cyclopoida
Infusoria
Radiolaria
Calanus
Acartia
Oithona-Oncaea type
Euchaeta
Centropages
Medusae
Ctenophora
Diaptomus
Insecta
Cyclops
deposit feeders
zooplankton
filter feeders
Holopedium
Limnephilus
Eiseniella
Mystacides
Lepidurus
Leptophlebia
Nemoura
Gammarus
Tripteroides
Culex
Uranotaenia
bacteria
Crustacea
Polychaeta
Bivalvia
Cumacea
Floridichthys carpio
Lophogobius cyprinoides
microzooplankton
gelatinous zooplankton
Caracolus caracolla
Psocoptera
Amphitritidae
Pectanaridae
Hylina veliei
Syllidae
Orbiniidae
Paraonidae
Spionidae
Cirratulidae
Capitellidae
Maldanidae
Aricidea
Jaspidella jaspidea
Nemertines
Nereidae
Hesionidae
Glyceridae
Onuphidae
Lagodon rhomboides
Laridae
Cyprinodon variegatus
Anatidae
Fundulus confluentus
Fundulus similis
Adinia xenica
sediment POC
Elasmopus levis
Lembos rectangularis
Acunmindeutopus naglei
Synchelidium
Ampithoe longimana
Cymadusa compta
Batea catharinensis
Listriella barnardi
Lysianopsis alba
Caprella penantis
Microfauna
meiofauna
Amphipoda
Tanaeidae
Mysidopsis
Ampelisca
Corophium
Cerapus tubularis
Gammarus mucronatus
Pagurus
Pagurus maclaughlinae
Pinixia floridana
Neopanope texana
Ophioderma brevispinum
Processa bermudiensis
Penaeus duoarum
Palaemonetes floridanus
Acteon punctostriatus
Cadulus carolinesis
Swartziella catesbyana
Acetocina candei
Truncatella pulchella
Nassarius vibex
Olivella mutica
Haminoea succinea

Based on studies in:
USA: Georgia (Marine)
USA: Maine (Lake or pond)
Scotland (Lake or pond)
New Zealand (Grassland)
Russia (Lake or pond)
South Africa (Desert or dune)
Finland (Lake or pond, Pelagic)
Pacific (Marine, Tropical)
Malaysia, W. Malaysia (Plant substrate)
unknown (Soil)
USA: Florida, Everglades (Estuarine)
Quebec (Lake or pond, Pelagic)
USA: Florida (Estuarine)
Malaysia (Swamp)
Netherlands: Wadden Sea, Ems estuary (Estuarine)
South Africa, Southwest coast (Marine)
Norway: Oppland, Ovre Heimdalsvatn Lake (Lake or pond)
Puerto Rico, El Verde (Rainforest)
Austria, Neusiedler Lake (Lake or pond)
Japan (Forest)
USA: Alaska (Tundra)

This list may not be complete but is based on published studies.
  • M. E. Vinogradov and E. A. Shushkina, Some development patterns of plankton communities in the upwelling areas of the Pacific Ocean. Mar. Biol. 48:357-366, from p. 359 (1978).
  • N. C. Morgan and D. S. McLusky, A summary of the Loch Leven IBP results in relation to lake management and future research, Proc. R. Soc. Edinburgh Series B 74:407-416, from p. 408 (1972).
  • A. C. Brown, Food relationships on the intertidal sandy beaches of the Cape Peninsula, S. Afr. J. Sci. 60:35-41, from p. 39 (1964).
  • T. Mizuno and J. I. Furtado, Food chain. In: Tasek Bera, J. I. Furtado and S. Mori, Eds. (Junk, The Hague, Netherlands, 1982), pp. 357-359, from p. 358.
  • Y. Kitazawa, Ecosystem metabolism of the subalpine coniferous forest of the Shigayama IBP area. In: Ecosystem Analysis of the Subalpine Coniferous Forest of Shigayama IBP Area, Central Japan, Y. Kitazawa, Ed. (Japanese Committee for the International Biol
  • J. Brown, Ecological investigations of the Tundra biome in the Prudhoe Bay Region, Alaska, Special Report, no. 2, Biol. Pap. Univ. Alaska (1975), from p. xiv.
  • E. A. Shushkina and M. E. Vinogradov, Trophic relationships in communities and the functioning of marine ecosystems: II. Some results of investigations on the pelagic ecosystem in tropical regions of the ocean. In: Marine Production Mechanisms, M. J. Dun
  • T. S. Petipa, Trophic relationships in communities and the functioning of marine ecosystems: I. Studies in trophic relationships in pelagic communities of the southern seas of the USSR and in the tropical Pacific. In: Marine Production Mechanisms, M. J. D
  • S. H. Hurlbert, M. S. Mulla, and H. R. Willson, Effects of an organophosphorus insecticide on the phytoplankton, zooplankton, and insect populations of freshwater ponds, Ecol. Monog. 42(1):269-299, from p. 293 (1972).
  • F. B. van Es, A preliminary carbon budget for a part of the Ems estuary: The Dollard, Helgolander wiss. Meeresunters. 30:283-294, from p. 292 (1977).
  • P. Larson, J. E. Brittain, L. Lein, A. Lillehammer and K. Tangen, The lake ecosystem of Ovre Heimdalsvatn, Holarctic Ecology 1:304-320, from p. 311 (1978).
  • R. A. Beaver, Fauna and food webs of pitcher plants in West Malaysia, The Malayan Nature Journal 33(1):1-10, from p. 8 (1979).
  • W. E. Odum and E. J. Heald, The detritus-based food web of an estuarine mangrove community, In Estuarine Research, Vol. 1, Chemistry, Biology and the Estuarine System, Academic Press, New York, pp. 265-286, from p. 281 (1975).
  • K. Paviour-Smith, The biotic community of a salt meadow in New Zealand, Trans. R. Soc. N.Z. 83(3):525-554, from p. 542 (1956).
  • A. Baril, Effect of the water mite Piona constricta on planktonic community structure, M.Sc. Thesis, University of Ottawa, Canada (1983).
  • J. Sarvala, Paarjarven energiatalous, Luonnon Tutkija 78(4-5):181-190, from p. 184 (1974).
  • C. Morley, Personal communication (1981).
  • J. M. Teal, Energy flow in the salt marsh ecosystem of Georgia, Ecology 43(4):614-624, from p. 616 (1962).
  • J. L. Brooks and E. S. Deevey, New England. In: Limnology in North America, D. G. Frey, Ed. (Univ. of Wisconsin Press, Madison, 1963), pp. 117-162, from p. 143.
  • Y. I. Sorokin, Biological productivity of the Rybinsk reservoir. In: Productivity Problems of Freshwaters, Z. Kajak and A. Hillbricht-Ilkowska, Eds. (Polish Scientific, Warsaw, 1972), pp. 493-503, from p. 497.
  • F. Schiemer, The benthic community of the open lake. In: Neusiedlersee: The Limnology of a Shallow Lake in Central Europe, H. L ffler, Ed. (Dr. W. Junk, The Hague, Netherlands, 1979), pp. 337-384, from p. 376.
  • Waide RB, Reagan WB (eds) (1996) The food web of a tropical rainforest. University of Chicago Press, Chicago
  • Christian RR, Luczkovich JJ (1999) Organizing and understanding a winter’s seagrass foodweb network through effective trophic levels. Ecol Model 117:99–124
  • Yodzis P (2000) Diffuse effects in food webs. Ecology 81:261–266
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Known prey organisms

bacteria (Benthic bacteria) preys on:
detritus
dissolved organic matter
allochthonous organic matter
phytoplankton
macrophytes
particulate organic matter
organic matter
soil organic matter
Insecta

bacteria
dung
sediment POC

Based on studies in:
Arctic (Marine)
Pacific (Marine)
Scotland (Lake or pond)
Portugal (Estuarine)
South Africa (Desert or dune)
Malaysia (Swamp)
Japan (Forest)
USA: Alaska (Tundra)
Netherlands: Wadden Sea, Ems estuary (Estuarine)
USA: Rhode Island (Marine)
Malaysia, W. Malaysia (Plant substrate)
USA: Florida, Everglades (Estuarine)
Puerto Rico, El Verde (Rainforest)
Quebec (Lake or pond, Pelagic)
Russia (Lake or pond)
Finland (Lake or pond, Pelagic)
Austria, Neusiedler Lake (Lake or pond)
South Africa, Southwest coast (Marine)
USA: Florida (Estuarine)
unknown (Soil)

This list may not be complete but is based on published studies.
  • M. J. Dunbar, Arctic and subarctic marine ecology: immediate problems, Arctic 7:213-228, from p. 223 (1954).
  • M. E. Vinogradov and E. A. Shushkina, Some development patterns of plankton communities in the upwelling areas of the Pacific Ocean. Mar. Biol. 48:357-366, from p. 359 (1978).
  • N. C. Morgan and D. S. McLusky, A summary of the Loch Leven IBP results in relation to lake management and future research, Proc. R. Soc. Edinburgh Series B 74:407-416, from p. 408 (1972).
  • L. Saldanha, Estudio Ambiental do Estuario do Tejo, Publ. no. 5(4) (CNA/Tejo, Lisbon, 1980).
  • A. C. Brown, Food relationships on the intertidal sandy beaches of the Cape Peninsula, S. Afr. J. Sci. 60:35-41, from p. 39 (1964).
  • T. Mizuno and J. I. Furtado, Food chain. In: Tasek Bera, J. I. Furtado and S. Mori, Eds. (Junk, The Hague, Netherlands, 1982), pp. 357-359, from p. 358.
  • Y. Kitazawa, Ecosystem metabolism of the subalpine coniferous forest of the Shigayama IBP area. In: Ecosystem Analysis of the Subalpine Coniferous Forest of Shigayama IBP Area, Central Japan, Y. Kitazawa, Ed. (Japanese Committee for the International Biol
  • J. Brown, Ecological investigations of the Tundra biome in the Prudhoe Bay Region, Alaska, Special Report, no. 2, Biol. Pap. Univ. Alaska (1975), from p. xiv.
  • E. A. Shushkina and M. E. Vinogradov, Trophic relationships in communities and the functioning of marine ecosystems: II. Some results of investigations on the pelagic ecosystem in tropical regions of the ocean. In: Marine Production Mechanisms, M. J. Dun
  • T. S. Petipa, Trophic relationships in communities and the functioning of marine ecosystems: I. Studies in trophic relationships in pelagic communities of the southern seas of the USSR and in the tropical Pacific. In: Marine Production Mechanisms, M. J. D
  • F. B. van Es, A preliminary carbon budget for a part of the Ems estuary: The Dollard, Helgolander wiss. Meeresunters. 30:283-294, from p. 292 (1977).
  • S. W. Nixon and C. A. Oviatt, Ecology of a New England salt marsh, Ecol. Monog. 43:463-498, from p. 491 (1973).
  • R. A. Beaver, Fauna and food webs of pitcher plants in West Malaysia, The Malayan Nature Journal 33(1):1-10, from p. 8 (1979).
  • W. E. Odum and E. J. Heald, The detritus-based food web of an estuarine mangrove community, In Estuarine Research, Vol. 1, Chemistry, Biology and the Estuarine System, Academic Press, New York, pp. 265-286, from p. 281 (1975).
  • A. Baril, Effect of the water mite Piona constricta on planktonic community structure, M.Sc. Thesis, University of Ottawa, Canada (1983).
  • J. Sarvala, Paarjarven energiatalous, Luonnon Tutkija 78(4-5):181-190, from p. 184 (1974).
  • C. Morley, Personal communication (1981).
  • Y. I. Sorokin, Biological productivity of the Rybinsk reservoir. In: Productivity Problems of Freshwaters, Z. Kajak and A. Hillbricht-Ilkowska, Eds. (Polish Scientific, Warsaw, 1972), pp. 493-503, from p. 497.
  • F. Schiemer, The benthic community of the open lake. In: Neusiedlersee: The Limnology of a Shallow Lake in Central Europe, H. L ffler, Ed. (Dr. W. Junk, The Hague, Netherlands, 1979), pp. 337-384, from p. 376.
  • Waide RB, Reagan WB (eds) (1996) The food web of a tropical rainforest. University of Chicago Press, Chicago
  • Christian RR, Luczkovich JJ (1999) Organizing and understanding a winter’s seagrass foodweb network through effective trophic levels. Ecol Model 117:99–124
  • Yodzis P (2000) Diffuse effects in food webs. Ecology 81:261–266
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Evolution and Systematics

Functional Adaptations

Functional adaptation

Microorganisms degrade crude oil: bacteria
 

Bacteria degrade crude oil more quickly when working in multi-species consortiums.

   
  "The data reported here supported the premise that faster rate of degradation of HCs is achieved by the action of assemblages of pure strains of microorganisms with overall broad enzymatic capabilities rather than by a single versatile organisms." (Adebusoye et al. 2007:1158)
  Learn more about this functional adaptation.
  • Adebusoye, S. A.; Ilori, M. O.; Amund, O. O.; Teniola, O. D.; Olatope, S. O. 2007. Microbial degradation of petroleum hydrocarbons in a polluted tropical stream. World Journal of Microbiology & Biotechnology. 23(8): 1149-1159.
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Functional adaptation

Microbes make natural polyester: bacteria
 

Bacteria manufacture biogedradable polyester by stringing together soluble monomers.

     
  "Bacteria make PHB [polyhydroxybutyrate] and other polyesters the same way nature makes starch: by stringing together soluble monomers and storing the finished polymer product in water-insoluble granules. When needed, the polymer in these granules--which, in the case of PHB, can take up to a whopping 85% of the cell's dry weight--can be broken down quickly and the building blocks reused for energetic or synthetic purposes.” (Yarnell 2004:27)
  Learn more about this functional adaptation.
  • Yarnell A. 2004. How bugs bag plastic. Chemical & Engineering News. 82(39): 27.
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Functional adaptation

Flagella aid locomotion: bacteria
 

The flagella of bacteria propel using a wheel and axle mechanism.

   
  "In electron micrographs, bacterial flagella look suspiciously like rigid, rotating propellers, driven by rotary engines in the bacterial surface beneath, as in figure 22.6. In a sense, they're not engines at all, leaving that to their basal motors. The combination consists of the only true rotary engine and propulsive unit known in the living world--a proper wheel and axle mechanism (Dusenbery 1996).

"They're far more efficient, at least in terms of power relative to weight, than ordinary flagella or even muscle, but they don't scale up, and nature hasn't used them elsewhere. Or at least she hasn't manufactured them elsewhere, since some higher organisms symbiotically appropriate bacteria for use as locomotory organelles." (Vogel 2003:449)



"Eukaryotic flagella and cilia have a remarkably uniform internal  'engine' known as the '9+2' axoneme. With few exceptions, the function  of cilia and flagella is to beat rhythmically and set up relative motion  between themselves and the liquid that surrounds them. The molecular  basis of axonemal movement is understood in considerable detail, with  the exception of the mechanism that provides its rhythmical or  oscillatory quality. Some kind of repetitive 'switching' event is  assumed to occur; there are several proposals regarding the nature of  the 'switch' and how it might operate.

"V. CONCLUSIONS

"(1) There are at least sixteen distinct circumstances that result in changes in the frequency of flagellar oscillation.Most of them appear to operate by affecting inter-doublet sliding velocity or by modulating the elasticity of flagellar structures.

"(2) Proposed explanations for the mechanism of the oscillation are presented under six headings. All the explanations have serious limitations.

"(3) Nevertheless, a provisional synthesis can been made, drawing on key experimental results. It proposes that the direction of sliding is the primary controlling factor for flagellar oscillation.

"(4) In detail, the provisional synthesis is that oscillation emerges from an effect of the direction of passive inter-doublet sliding on (a) the force-generating cycles of dynein (perhaps the ATPase rate) and (b) dyneinto- dynein synchronisation along a doublet. Dyneins actively generate force when sliding in one direction is detected, and are inhibited from doing so by the detection of sliding in the other direction. The direction of the initial, passive sliding oscillates because it is regulated hydrodynamically by the direction of the propulsive thrust. However, a supplementary mechanism seems to exist, namely a mechanically induced reversal of sliding direction due to the recoil of elastic structures deformed in response to the preceding active sliding displacement." (Woolley 2010:453,467)
  Learn more about this functional adaptation.
  • Steven Vogel. 2003. Comparative Biomechanics: Life's Physical World. Princeton: Princeton University Press. 580 p.
  • Woolley DM. 2010. Flagellar oscillation: a commentary on proposed mechanisms. Biological Reviews. 85(3): 453–470.
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Functional adaptation

Transporting electrons extracellularly: sediment bacteria
 

Sediment bacteria may link distant chemical reactions using nanowires to transport electrons.

       
 

"Bacteria lurking in sediment at the bottom of the sea are pulling off  a clever trick — using an electric current to link together the  chemical reactions of oxygen in water with those of sediment nutrients  deeper down.

 

"Lars Peter Nielsen at Aarhus University in Denmark and his  colleagues suggestthat a chain of bacteria work together to transport electrons from a  marine sediment to the overlying water up to two centimetres away. The  electrons are produced by reactions between organic matter and hydrogen  sulphide in the sediment, and transported to the sediment surface where  they react with oxygen.

 

"This means that throughout the entire system, the top layers of  sediment 'breathe' for the whole, and those at the bottom 'eat' for the  whole.

 

"The research helps to add weight to a suggestion within the  geophysics and microbiology communities that bacteria can grow tiny  'wires' and hook up to form a biogeobattery — a giant natural battery  that generates electrical currents." (Sanderson 2010)


  Learn more about this functional adaptation.
  • Nielsen LP; Risgaard-Petersen N; Fossing H; Christensen PB; Sayama M. 2010. Electric currents couple spatially separated biogeochemical processes in marine sediment. Nature. 463: 1071-1074.
  • Sanderson K. 2010. Bacteria buzzing in the seabed. Nature News [Internet],
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Functional adaptation

Communication molecules coordinate behavior: chronic wound bacteria
 

Pathogenic bacteria in chronic wounds communicate using signaling molecules.

       
  "'Bacteria, often viewed as simplistic creatures, are in fact very  sociable units of life,' said Alex Rickard, assistant professor of  biological sciences [at Binghamton University]. 'They can physically and chemically interact with  one another and are quite selective about who they hang out with. How  bacteria might communicate in chronic wounds, however, was somewhat of a  mystery.' 

"Working with researchers and physicians at the Center for Biofilm  Engineering at Montana State University and the Southwest Regional Wound  Care Center in Lubbock, Texas, Rickard and a team of undergraduates  were able to identify specific types of chronic wound bacteria and to  test their ability to produce cell-cell signaling molecules.

 

"close to  70 percent ofchronic wound strains produce a specific type of  communication molecule – autoinducer-2 (AI-2). A smaller percentage –  around 20 percent – produce a different type of communication molecule,  called acyl-homoserine-lactones (AHLs). Scientists already know that  structurally different bacterial cell-cell signaling molecules are able  to mediate cell-cell communication, including AI-2 and AHLs.

 

"'Based on our findings, we think that most resident species – the 'good' bacteria that live on us and don't cause disease – produce AI-2,  while the pathogenic species typically produce AHLs,' said Katelynn  Manton, who was part of the undergraduate team and is now pursuing her  doctorate. 'And it didn't seem to matter what kind of chronic wound we  looked at – diabetic ulcers, vascular ulcers or environmentally induced  chronic wounds. They all indicated a presence of possible AHLs or  AI-2s.'

 

"According to Rickard and his team, the typically pathogenic bacteria  communicate in one language; the 'good' bacteria in another. The big  question now is whether any of them are bilingual and can listen in on  one another's 'conversations.' Being able to interpret – or perhaps even  guide – these cell-cell signals could influence wound development." (Glover 2010) 


  Learn more about this functional adaptation.
  • Rickard AH; Colacino KR; Manton KM; Morton RI; Pulcini E; Pfeil J; Rhoads; Wolcott RD; James G. 2009. Production of cell–cell signalling molecules by bacteria isolated from human chronic wounds. Journal of Applied Microbiology. 108(5): 1509-1522.
  • Glover G. 2010. Bacterial 'eavesdropping' offers hope for chronic wounds. DISCOVER-e Binghamton University News [Internet],
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Functional adaptation

Membranes distinguish sweet from sour: colon bacilli
 

The membrane of colon bacilli cells find sweet-tasting chemicals and avoid bitter or sour ones via sensory proteins.

   
  "Chemoreception occurs even in unicellular organisms…Protozoa such as amoebae and microbes such as colon bacilli show chemotaxis; they gather and escape from some chemical substances. The former is called positive chemotaxis and the latter negative chemotaxis. Colon bacilli show positive chemotaxis for amino acids tasting sweet and negative chemotaxis for chemical substances tasting strongly bitter or sour. This behavior is quite reasonable because substances tasting sweet become energy sources for living organisms whereas substances tasting strongly bitter or sour are often harmful." (Toko 2000:26)
  Learn more about this functional adaptation.
  • Toko, Kiyoshi. 2000. Biomimetic sensor technology. Cambridge, UK: Cambridge University Press.
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Functional adaptation

Colonies self-assemble: bacteria
 

Bacterial colonies that form stromatolites self-assemble by making independent decisions while maintaining communication.

   
  "Stromatolites are colonies of bacteria that self-assemble into rock formations in tidal salt flats. Each stromatolite can make independent decisions, while maintaining communication with the colony. The workload is shared among all colony individuals. Stromatolites breed rapidly, and quickly develop resistance to antibiotics and other threats by developing new genes. Ian Marshall plans to incorporate these principles into the next wave of BT network management. Like the stromatolites, each element of BT's [British Telecom] network will be able to make independent decisions, yet will remain fully communicative with neighbors. Workload--i.e., incoming calls--will be spread evenly through the network. And in a process mimicking natural selection, desirable services will be quickly distributed to BT customers, while undesirable services die out." (Courtesy of the Biomimicry Guild)
  Learn more about this functional adaptation.
  • Atkinson S; Williams P. 2009. Quorum sensing and social networking in the microbial world. J R Soc Interface. 6(40): 959-78.
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Functional adaptation

Enzymes allow cellulose digestion: bacteria
 

Symbiotic bacteria digest cellulose with the help of enzymes.

   
  "Those that have become specialist leaf-feeders can only extract nourishment from it by enlisting the aid of a very different kind of living organism--bacteria. They, unlike any animal, can digest cellulose." (Attenborough 1995: 58)
  Learn more about this functional adaptation.
  • Attenborough, D. 1995. The Private Life of Plants: A Natural History of Plant Behavior. London: BBC Books. 320 p.
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Functional adaptation

Proteins limit nanoparticle dispersal: sulfate-reducing bacteria
 

Extracellular proteins of some sulfate-reducing bacteria limit the dispersal of nanoparticles by aggregating them.

     
  Analysis revealed an "intimate association of proteins with spheroidal aggregates of biogenic zinc sulfide nanocrystals, an example of extracellular biomineralization. Experiments involving synthetic zinc sulfide nanoparticles and representative amino acids indicated a driving role for cysteine in rapid nanoparticle aggregation. These findings suggest that microbially derived extracellular proteins can limit the dispersal of nanoparticulate metal-bearing phases, such as the mineral products of bioremediation, that may otherwise be transported away from their source by subsurface fluid flow." (Moreau et al. 2007:1600, 1602)
  Learn more about this functional adaptation.
  • Moreau JW, Weber PK, Martin MC, Gilbert B, Hutcheon ID, Banfield JF. 2007. Extracellular Proteins Limit the Dispersal of Biogenic Nanoparticles. Science. 316(5831): 1600-1603.
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Functional adaptation

Extremophile converts fatty-acids into energy: bacteria
 

Metabolic process of extremophile bacteria converts fatty acids into a variety of secondary compounds, including hydrogen, by running normal metabolism backwards.

   
  "It survives on a food so unrewarding it needs help disposing of its waste. Eking out an existence only by turning the normal chemistry of life back to front, the bacterium Syntrophus aciditrophicus is one of the most extreme-living organisms known. Now its genome has been sequenced and is yielding clues as to how it survives. It might even help us make hydrogen from waste. Robert Gunsalus of the University of California, Los Angeles, and colleagues identified 3169 genes in Syntrophus. The bacterium performs a key part of the carbon cycle by breaking down fatty acids--used by almost no other organisms as an energy source. To do this, its genes stand normal energy-generation reactions on their head (Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.0610456104). In normal respiration, organic compounds are oxidised, and the electrons this liberates are used to drive the production of the energy-storage molecule ATP. In Syntrophus the electrons go the opposite way as the bacterium turns fatty acids into a variety of breakdown products that it feeds on, plus hydrogen and the chemical formate. It survives only with the 'help' of other bacteria that hoover up the hydrogen and formate--otherwise it could not feed. Understanding the bacterium's metabolism will 'hopefully make biohydrogen production a reality', says Gunsalus." (Hooper 2007: 12) from issue 2600 of New Scientist magazine, 21 April 2007, page 12)
  Learn more about this functional adaptation.
  • Hooper, R. 2007. Extreme bacteria run chemistry of life in reverse. New Scientist. 194(2600): 12-12.
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Functional adaptation

Hairlike extensions responsible for movement: bacteria
 

Some bacteria move by attaching and then retracting pili through their outer membranes.

   
  "Gliding motion across surfaces, usually with slime--whether or not by the same scheme--occurs in procaryotic organisms (bacteria and their kin) as well. It's based on either of two mechanisms. Bacteria are often covered with tiny hairs, pili; retraction of one type (designated IV) through their outer membranes can move them around. Alternatively, they can secrete carbohydrate slime rearward to get a push (Kaiser 2000; Merz and Forest 2002)." (Vogel 2003:450)
  Learn more about this functional adaptation.
  • Steven Vogel. 2003. Comparative Biomechanics: Life's Physical World. Princeton: Princeton University Press. 580 p.
  • Merz, AJ; Forest, KT. 2002. Bacterial surface motility: slime trails, grappling hooks, and nozzles. Current Biology. 12: R297-R303.
  • Kaiser, D. 2000. Bacterial motility: how do pili pull?. Current Biology. 10(21): R777-R780.
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Functional adaptation

Shape-shifting aids swimming: bacteria
 

Body of bacteria moves through water by shape-shifting.

   
  "On the scale of a bacterium, water is as viscous as treacle. This makes swimming difficult because a simple symmetrical stroke gets you nowhere: the recovery stroke pushes you as far back as the first part of the stroke pulled you forward. So these bacteria adopt different geometrical shapes during the first and second parts of the stroke to maximise the forward movement. Swimming robots and moving parts in nanomachines are already engineered in this way." (Hogan 2003:24)
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  • Hogan, Jenny. 2003. Shape-shifter beats the laws of physics. New Scientist. (2385):
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Functional adaptation

Membranes avoid freezing: bacteria
 

Membranes of some microbes continue to allow diffusion at cold temperatures by having a special fatty composition that keep them relatively fluid.

   
  "Bacteria have two skins, an outer one which is a stiff molecular mesh, through which molecules of food and water can diffuse fairly easily, and an inner one, elastic and membranous, which has to be very selectively permeable, so that nutrients can get in but the internal substances of the cell do not leak out. (This, by the way, is the skin which ice damages lethally; the outer layer is tougher and serves to keep out big molecules and to sustain the cell's shape). The cell membrane, as it is called, includes a lot of fat in its structure, and its permeability is very much influenced by fluidity of that fat…Psychrophiles have cell membranes of a special fatty composition, such that they are relatively fluid at temperatures near freezing point--and again they pay a price: their membranes become too fluid, and begin to melt, when the environment warms to the temperatures that most bacteria prefer." (Postgate 1994:28)
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  • Postgate, JR. 1994. The outer reaches of life. Cambridge (Great Britain): Cambridge University Press. 276 p.
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Functional adaptation

By-products inhibit yeast and fungi: Pseudomonas aeruginosa
 

The metabolism of Pseudomonas aeruginosa produces products that inhibit yeast and fungal growth via the conversion of unsaturated fatty acids.

     
  "Bioconversion is a “green” technology that converts fatty acids into entirely new chemical compounds with antimicrobial, industrial or biomedical properties. The bioconversion reactions by Pseudomonas aeruginosa PR3 have been cited extensively among microbial systems that produce mono-, di- and tri-hydroxy fatty acid derivatives from unsaturated fatty acids (Kuo et al., 1998). Strain PR3, isolated from a waste water stream on a pig farm in Morton, IL, USA was found to convert oleic acid to a novel compound, 7,10-dihydroxy-8(E)-octadecenoic acid (DOD), which inhibits the laboratory growth of Candida albicans, a yeast that sometimes causes thrush and other infections in humans (Hou and Bagby, 1991). This strain was also found to convert ricinoleic acid to another novel compound 7,10,12-trihydroxy-8(E)-octadecenoic acid (TOD), which inhibits the rice blast fungus, raising the prospect for a biological fungicide against this pathogen (Kuo et al., 2001). These recently described compounds, from the microbial conversion of unsaturated fatty acids, are potential value-added products that will inhibit such pathogens." (Bajpai et al. 2008:136)
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  • Bajpai, Vivek K.; Shin, Seung Yong; Kim, Hak Ryul; Kang, Sun Chul. 2008. Anti-fungal action of bioconverted eicosapentaenoic acid (bEPA) against plant pathogens. Industrial Crops and Products. 27(1): 136-141.
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Functional adaptation

Storing carbon and energy: bacteria
 

Bacteria store carbon and energy by synthesizing a polymer known as poly(beta-hydroxybutyrate) or PHB.

       
  "Geoffrey Coates and others at Cornell University have discovered a highly efficient chemical route for synthesis of a polymer known as poly(beta-hydroxybutyrate) or PHB, a thermoplastic polyester found in nature, particularly in some bacteria. Bacteria use it as a storage form of carbon and energy. According to Coates's website...'Poly(hydroxyalkanoate)s (PHAs) are naturally-occurring biodegradable polyesters that are presently commercially made by fermentation. We are working to develop an alternate route that consists of carbonylation of epoxides to beta-lactones, followed by ring-opening polymerization to yield PHAs. A key advance in our lab regarding this strategy was the discovery of epoxide carbonylation catalysts consisting of Lewis-acidic cations in combination with Co(CO)4 anions. These highly active and selective catalysts carbonylate a wide range of epoxides and lactones to their corresponding lactones and anhydrides. Current work focuses on the elucidation of their mechanisms of operations, and the development of more active and stereoselective variants of these catalysts.'" (Courtesy of the Biomimicry Guild)
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Functional adaptation

Slime enables movement: bacteria
 

Some bacteria move by 'pushing' off secreted carbohydrate slime.

   
  "Gliding motion across surfaces, usually with slime--whether or not by the same scheme--occurs in procaryotic organisms (bacteria and their kin) as well. It's based on either of two mechanisms. Bacteria are often covered with tiny hairs, pili; retraction of one type (designated IV) through their outer membranes can move them around. Alternatively, they can secrete carbohydrate slime rearward to get a push (Kaiser 2000; Merz and Forest 2002)." (Vogel 2003:450)
  Learn more about this functional adaptation.
  • Steven Vogel. 2003. Comparative Biomechanics: Life's Physical World. Princeton: Princeton University Press. 580 p.
  • Merz, AJ; Forest, KT. 2002. Bacterial surface motility: slime trails, grappling hooks, and nozzles. Current Biology. 12: R297-R303.
  • Kaiser, D. 2000. Bacterial motility: how do pili pull?. Current Biology. 10(21): R777-R780.
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Functional adaptation

Enzymes detoxify mercury compounds: bacteria
 

The enzymatic system of aerobic bacteria detoxifies mercury compounds such as methyl-mercury via the enzymes organomercurial lyase (MerB) and mercuric ion reductase.

   
  "Mercury is well known for its toxicity to living organisms. Inorganic mercuric compounds (HgX2) and organomercurials (R-Hg-X), in which the Hg is formally in the +2 oxidation state, are primarily responsible for the toxicity…Elemental mercury itself (Hg0) has little affinity for cellular ligands and is toxic only if it becomes oxidized to the +2 state in the cell…aerobic bacteria have evolved the ingenious strategy of eliminating mercuric and organomercurial compounds from their environment through reduction of Hg2+ to Hg0. To accomplish this, they couple the activity of two enzymes: organomercurial lyase (MerB) and mercuric ion reductase." (Miller 2007:537)

"Accumulation of extremely toxic methylmercury in the environment—particularly in fish—has triggered an effort by scientists to unravel the process by which a set of bacterial enzymes capture and then detoxify the compound. In a new development, Jonathan G. Melnick and Gerard Parkin of Columbia University report a synthetic mercury complex that provides insight into how one of these enzymes catalyzes cleavage of the Hg-C bond (Science 2007, 317, 225). The finding is expected to boost efforts to genetically modify plants to sequester HgCH3+ for environmental cleanup. In nature, microbes synthesize HgCH3+ from naturally occurring Hg2+, as well as from mercury released in the emissions of coal-fired power plants. Organomercury compounds are toxic because the metal has a high affinity for sulfur, in particular the sulfur of thiol (-SH) groups in cysteine units of proteins. Once the mercury binds, the normal function of the proteins is disrupted. Bacteria resistant to HgCH3+ toxicity produce an enzyme named MerB, which has three cysteine residues in its active site that are known to be crucial for cleaving the Hg-C bond. But the exact way in which MerB coordinates to HgCH3+ and the 'intimate details of the reaction mechanism' have been a mystery, Parkin says. (A second enzyme, MerA, reduces the resulting Hg2+ to less toxic elemental mercury.) Melnick and Parkin thus set out to decipher the mechanism of action of MerB. Melnick and Parkin 'provide an elegant atomic-level description for the facile cleavage of a carbon-mercury bond,' notes James G. Omichinski of the University of Montreal in a Science commentary. Their observations provide valuable insight into the basic mechanism of MerB's activity, he adds. Considerable work remains to be done, but understanding this mechanism 'is essential to efforts to reengineer MerB to improve its catalytic efficiency for the bioremediation of methylmercury,' Omichinski writes." (Ritter 2007:10)
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  • Miller, Susan M. 2007. Cleaving C-Hg bonds: two thiolates are better than one. Nat Chem Biol. 3(9): 537-538.
  • Ritter, Steve. 2007. Methylmercury Detox. Chemical & Engineering News [Internet],
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Functional adaptation

Chemicals made with natural ingredients: bacteria
 

Bacteria can use natural chemicals to create complex molecules, including antibiotics, with special enzymes.

     
  "Until now, only the intricate machinery inside cells could take a mix of enzyme ingredients, blend them together and deliver a natural product with an elaborate chemical structure such as penicillin. Researchers at UC San Diego's Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences and the University of Arizona have for the first time demonstrated the ability to mimic this process outside of a cell.

"A team led by Qian Cheng and Bradley Moore of Scripps was able to synthesize an antibiotic natural product created by a Hawaiian sea sediment bacterium. They did so by combining a cocktail of enzymes, the protein catalysts inside cells, in a relatively simple mixing process inside a laboratory flask…The antibiotic synthesized in Moore's laboratory, called enterocin, was assembled in approximately two hours. Such a compound would normally take months if not a year to prepare chemically." (Scripps News Service 2007)
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Functional adaptation

Enzyme catalyzes many reactions: plants
 

Many plants and microorganisms can catalyze a wide variety of organic chemical reactions via the 2OG oxygenase enzyme.

     
  "In plants and microorganisms…2OG oxygenases catalyze a plethora of oxidative reactions, which has led to the proposal that they may be the most versatile of all oxidizing biological catalysts. Some of these reactions are chemically remarkable and indeed presently cannot be achieved through synthetic—that is, non-biological—chemistry. Oxidative reactions catalyzed by 2OG oxygenases include cyclizations, ring fragmentation, C-C bond cleavage, epimerization, desaturation and the hydroxylation of aromatic rings. The discovery that 2OG oxygenases can catalyze chlorination reactions further extends the scope of the family." (Flashman 2007:86)
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  • Flashman, Emily; Schofield, Christopher J. 2007. The most versatile of all reactive intermediates?. Nat Chem Biol. 3(2): 86-87.
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