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**mesocosm** · 02-10-2006, 08:57 PM

Greetings All !

If you've ever wondered what terms such as bacteria, archaea, photoautotroph, photoheteroautotroph, chemautotroph, chemoheterotroph, obligate, facultative actually mean ... this is an excellent read. It contains one of the best descriptions on how bacteria and biofilms "feed" that I've come across on the internet.

Isolation, Nutrition, and Cultivation of Microorganisms
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**mesocosm** · 02-10-2006, 08:59 PM

Greetings All !

If you've ever wondered how bacteria generate surfactants and participate in flocculation processes, this is a relatively good read. If you're interested in the biochemistry of how bacteria might be participating the the creation of a crystal clear water column, this is a very good read.

Microbial production of biosurfactants and their importance.

N. G. K. Karanth, P. G. Deo and N. K. Veenanadig

Pesticide Residue Abatement Lab, Food Protectants and Infestation Control Department, Central Food Technological Research Institute,Mysore 570 013, India

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**mesocosm** · 02-10-2006, 09:03 PM

Greetings All !

Bacteria actively uptake amino acids ...

Bioenergetics of marine bacteria--respiration-coupled Na+ pump.

Yakugaku Zasshi. 2000 Jan;120(1):16-27.
Laboratory of Membrane Biochemistry, Faculty of Pharmaceutical Sciences Chiba University, Japan.

Review ... not an abstract ...

Marine bacteria are unique in the requirement for Na+ for optimal growth. Using a marine bacterium Vibrio alginolyticus, it was confirmed that Na+ is essential for the active uptake of all amino acids. Furthermore, the respiratory chain of V. alginolyticus was found to require Na+ for the maximum activity. The site of Na(+)-dependent activation is localized in the NADH-quinone reductase segment, where Na+ is extruded from the cells as a direct result of redox reaction. Thus, marine bacteria are able to directly generate sodium-motive force by respiratory chain activity. The sodium-motive force is directly coupled to the active uptake of nutrients and to the rotation of polar flagella. In addition to the energy coupling by proton circulation, marine bacteria are unique in utilizing Na+ circulation for the energy coupling. The latter mode of energy coupling is superior to proton circulation especially at alkaline and Na(+)-rich conditions. The respiration-coupled Na+ pump is widely distributed among Gram-negative marine and moderately halophilic bacteria. Recently, it was found that the same type of Na+ pump is distributed in the Gram-negative pathogenic bacteria. Since the presence of Na+ pump widens the adaptability of bacteria to grow at harsh environments, Na+ pump is likely to be helpful for the growth of pathogenic bacteria in the host cells to manifest their pathogenicity.

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**mesocosm** · 02-10-2006, 09:08 PM

Greetings All !

Some bacteria do some interesting things with phosphate ...

Atypical Polyphosphate Accumulation by the Denitrifying Bacterium Paracoccus denitrificans.
Yoram Barak and Jaap van Rijn

Abstract

Polyphosphate accumulation by Paracoccus denitrificans was examined under aerobic, anoxic, and anaerobic conditions. Polyphosphate synthesis by this denitrifier took place with either oxygen or nitrate as the electron acceptor and in the presence of an external carbon source. Cells were capable of poly--hydroxybutyrate (PHB) synthesis, but no polyphosphate was produced when PHB-rich cells were incubated under anoxic conditions in the absence of an external carbon source. By comparison of these findings to those with polyphosphate-accumulating organisms thought to be responsible for phosphate removal in activated sludge systems, it is concluded that P. denitrificans is capable of combined phosphate and nitrate removal without the need for alternating anaerobic/aerobic or anaerobic/anoxic switches. Studies on additional denitrifying isolates from a denitrifying fluidized bed reactor suggested that polyphosphate accumulation is widespread among denitrifiers.

Extracted from:
Applied and Environmental Microbiology, March 2000, p. 1209-1212, Vol. 66, No. 3

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**mesocosm** · 02-10-2006, 09:11 PM

Greetings All !

Bacteria can do some interesting things with iron ...

Anaerobic Respiration Using Fe3+, S, and H2 in the Chemolithoautotrophic Bacterium Acidithiobacillus ferrooxidans.

Naoya Ohmura, Kazuhiro Sasaki, Norio Matsumoto, and Hiroshi Saiki

Abstract

The chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans has been known as an aerobe that respires on iron and sulfur. Here we show that the bacterium could chemolithoautotrophically grow not only on H2/O2 under aerobic conditions but also on H2/Fe3+, H2/S, or S0/Fe3+ under anaerobic conditions. Anaerobic respiration using Fe3+ or S as an electron acceptor and H2 or S as an electron donor serves as a primary energy source of the bacterium. Anaerobic respiration based on reduction of Fe3+ induced the bacterium to synthesize significant amounts of a c-type cytochrome that was purified as an acid-stable and soluble 28-kDa monomer. The purified cytochrome in the oxidized form was reduced in the presence of the crude extract, and the reduced cytochrome was reoxidized by Fe3+. Respiration based on reduction of Fe3+ coupled to oxidation of a c type cytochrome may be involved in the primary mechanism of energy production in the bacterium on anaerobic iron respiration.

Extracted from:
Journal of Bacteriology, April 2002, p. 2081-2087, Vol. 184, No. 8

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**mesocosm** · 02-10-2006, 09:16 PM

Greetings All !

If you're interested in understanding the actual biochemical mechanisms of nitrification and denitrification ... among other things ... you might wish to consider reviewing the relationships between "electron donors" and "electron acceptors" ...

Electron Donor

An electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process.

Electron donors give up or donate an electron during cellular respiration, resulting in the release of energy. Microorganisms, such as bacteria, obtain energy to grow by transferring electrons from an electron donor to an electron acceptor. The microorganism through its cellular machinery collects the energy for its use. The final result is the electron is donated to an electron acceptor. During this process (electron transport chain) the electron donor is oxidized and the electron acceptor is reduced. Petroleum hydrocarbons, less chlorinated solvents like vinyl chloride, soil organic matter, and reduced inorganic compounds are all compounds that can act as electron donors. These reactions are of interest not only because they allow organisms to obtain energy, but also because they are involved in the natural biodegradation of organic contaminants. When clean-up professionals use monitored natural attenuation to clean up contaminated sites, biodegradation is one of the major contributing processes.

Extracted from:
Wikipedia

Electron Acceptor

An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that, by virtue of its accepting electrons, is itself reduced in the process.

A terminal electron acceptor is a compound that receives or accepts an electron during cellular respiration or photosynthesis. Microorganisms such as bacteria obtain energy to grow by transferring electrons from an electron donor to an electron acceptor. The microorganism through its cellular machinery collects the energy for its use. The process starts with the transfer of an electron from an electron donor. During this process (electron transport chain) the electron acceptor is reduced and the electron donor is oxidized. Examples of acceptors include oxygen, nitrate, iron (III), manganese (IV), sulfate, carbon dioxide, or in some cases the chlorinated solvents such as tetrachloroethene (PCE), trichloroethene (TCE), dichloroethene (DCE), and vinyl chloride (VC). These reactions are of interest not only because they allow organisms to obtain energy, but also because they are involved in the natural biodegradation of organic contaminants. When clean-up professionals use monitored natural attenuation to clean up contaminated sites, biodegradation is one of the major contributing processes.

Extracted from:
Wikipedia

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**mesocosm** · 02-10-2006, 09:19 PM

Greetings All !

Denitrifiers can use ferrous iron as an electron donor ...

Anaerobic, Nitrate-Dependent Microbial Oxidation of Ferrous Iron
KL Straub, M Benz, B Schink and F Widdel

Abstract

Enrichment and pure cultures of nitrate-reducing bacteria were shown to grow anaerobically with ferrous iron as the only electron donor or as the additional electron donor in the presence of acetate. The newly observed bacterial process may significantly contribute to ferric iron formation in the suboxic zone of aquatic sediments.

Extracted from:
Appl. Environ. Microbiol., Apr 1996, 1458-1460, Vol 62, No. 4

Abstract

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**mesocosm** · 02-10-2006, 09:23 PM

Greetings All !

In the "early days" of ZEOvit product discussions, one of the chemicals that
occassionally appeared as a candidate for a carbon source for bacteria was acetate ...

Influence of Volatile Fatty Acids on Nitrite Accumulation by a Pseudomonas stutzeri Strain Isolated from a Denitrifying Fluidized Bed Reactor

J van Rijn, Y Tal and Y Barak

Abstract

Intermediate nitrite accumulation during denitrification by Pseudomonas stutzeri isolated from a denitrifying fluidized bed reactor was examined in the presence of different volatile fatty acids. Nitrite accumulated when acetate or propionate served as the carbon and electron source but did not accumulate in the presence of butyrate, valerate, or caproate. Nitrite accumulation in the presence of acetate was caused by differences in the rates of nitrate and nitrite reduction and, in addition, by competition between nitrate and nitrite reduction pathways for electrons. Incubation of the cells with butyrate resulted in a slower nitrate reduction rate and a faster nitrite reduction rate than incubation with acetate. Whereas nitrate inhibited the nitrite reduction rate in the presence of acetate, no such inhibition was found in butyrate-supplemented cells. Cytochromes b and c were found to mediate electron transport during nitrate reduction by the cells. Cytochrome c was reduced via a different pathway when nitrite-reducing cells were incubated with acetate than when they were incubated with butyrate. Furthermore, addition of antimycin A to nitrite-reducing cells resulted in partial inhibition of electron transport to cytochrome c in acetate-supplemented cells but not in butyrate-supplemented cells. On the basis of these findings, we propose that differences in intermediate nitrite accumulation are caused by differences in electron flow to nitrate and nitrite reductases during oxidation of either acetate or butyrate.

Extracted from:
Appl. Environ. Microbiol., Jul 1996, 2615-2620, Vol 62, No. 7

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**mesocosm** · 02-10-2006, 09:26 PM

Greetings All !

If you're interested in a general overview of biofilms, this might be useful to you ...

Microbial Biofilms: from Ecology to Molecular Genetics

Mary Ellen Davey and George A. O'toole
Microbiology and Molecular Biology Reviews, December 2000, p. 847-867, Vol. 64, No. 4

From the summary ...

"Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. ..."

[ Hyper-Linked Table of Contents for the Article:]
SUMMARY
INTRODUCTION
Complex Attached and Aggregated Communities
Collective Behavior
SURFACE-ATTACHED COMMUNITIES IN THE REAL WORLD
Biofilm Structure
Structure and Function Studies
Plant-Associated Biofilms
ECOLOGICAL ADVANTAGES: WHY MAKE A BIOFILM?
Protection from the Environment
Nutrient Availability and Metabolic Cooperativity
Acquisition of New Genetic Traits
ROLE OF SURFACE-ATTACHED BACTERIA IN DISEASE
Bacterial Biofilm Infections
Implant-Based Infections
Biofilms and Pathogenesis
GENETIC DISSECTION OF BIOFILM FORMATION
Role of Environmental Signals
Initiation of Biofilm Formation
Maturation of the Biofilm
Molecular Genetics of Oral Biofilms
CONCLUSIONS
ACKNOWLEDGMENTS
REFERENCES

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**mesocosm** · 02-11-2006, 08:37 AM

Greetings All !

Having trouble searching the web for references on "mulm"? Try using the keywords "aggregates", or, "microaggregates" instead ...

In 1995, an extensive investigation was carried out in the Elbe Estuary from Hamburg to the German Bight. Special attention was paid to aggregates and their colonization by micro-organisms. Such aggregates are well known from marine and lake environments and called "marine" or "lake snow". My results show that colonization by bacteria and protozoans is fairly similar to those of marine and lake snow. The composition of the aggregates reflects the structure of the plankton community in the water. The abundance of aggregates varied between 10 and 225 aggregates 1-1 and their size ranged from 10 µm to 5000 µm. Aggregates that were very abundant and small in size were present in the coastal area, whereas larger aggregates were present in the upstream parts of the estuary. Limnetic and marine aggregates were richly colonized by different organisms. The highest concentrations of aggregates with little colonization were encountered in the turbid zone of the estuary. A special technique was used to isolate single aggregates and to investigate their colonization by bacteria and protozoans, such as amoebas, ciliates and flagellates. The aggregates were densely colonized by micro-organisms, and their abundance per unit volume was 4.0 x 103 greater than that in the pelagic water.

Extracted from:

The diversity of the microbial community on microaggregates in the Elbe Estuary

Heike Zimmerman, 1997
Institut für Hydrobiologie und Fischereiwissenschaft, Universität Hamburg, Zeiseweg 9, D-22765 Hamburg

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**mesocosm** · 02-11-2006, 08:43 AM

Greetings All !

Inoculating ecosystems with bacteria may have a "probiotic" effect ...

Growth of organisms is often limited by particular nutirents and it has during the last decade been suggested that iron is the factor limiting biomass production in the marine environment. As free iron is limited, most organisms have developed highly specialized chelating systems. The purpose of this study was to investigate the role of iron limitation and abilty to chelate this metal in the interaction between aquatic bacteria.

Using the universal chrome azurol S assay, aquatic pseudomonads are shown to chelate iron very efficiently by production of extracellular siderophores. By screening in well diffusion assay, testing of culture supernatants and co-culture in microcosm, we show that aquatic pseudomonads are able to inhibit growth of other aquatic bacteria, particularly under iron limited conditions. The ability to chelate iron is an essential virulence factor and most diseases progress faster if the host is overloaded with iron. Thus, a high content of iron in fish feed has been shown to increase disease frequency. The fish pathogenic bacteria, Vibrio anguillarum and Aeromonas salmonicida, were both inhibited by siderophore producing aquatic pseudomonads and it is hypothesized that inhibitory, non-pathogenic pseudomonads may be used as probiotic treatment in fish farming.

Extracted from:

Inhibition of fish pathogenic bacteria by aquatic pseudomonads under iron limited conditions

L. Gram, 1997
Danish Institute for Fisheries Research, Department of Seafood Research, Danish Technical University bldg. 221, DK-2800 Lyngby, Denmark

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**mesocosm** · 02-11-2006, 08:59 AM

Greetings All !

Introducing particulate "food" into a bacterial community can alter the behavior of primary producer and primary consumer "webs" ... not just in terms of the bacterial community itself, but also in terms of the population and succession of microorganisms associated with the bacterial community. Folks considering dosing phytoplankton into their ecosystems might be interested in this one ... JMO.

Microbiological degradation of phytoplankton blooms was studied ex-perimentally using diatome Skeletonema costatum prekilled culture as detritial-substrate for marine microbial community. Qualitative and quantitative changes of the microbial community and algal detritus structure were determined by microscopic examinations and microbial activity measurements over an incubation period of 11 days. Most of the bacterial parameters (number of total and attached cells, biomass, mean cell volume and production) were the highest after 24 h incubation. Bacterial peak (3.63·106 cells ml-1; production 0.77 ·106 cells ml-1h-1) was followed by rapid increase in the number of microflagellates (2.55·105 cells ml-1) which in turn declined after ciliates appeared in the succession. The amount of attached bacteria ranged from 0.6 to 24.9 % of the total bacterial population. The maximum value of this parameter appeared 24 h after the maximums of total and free bacterial abundance. The later stage of the succession was characterized by a mixed community of bacteria, flagellates and ciliates with numerical ratio of 1000:1.8:0.2 which was similar to the same ratio in the control seawater samples, incubated without phytodetritus addition. Microbial community stabilization and structural changes of phytodetritial particles (breakdown, aggregation) indicated that Skeletonema bloom, initial density 52.6·103 cells ml-1, can be utilized by pelagic microheterotrophs within 10 days at water temperature 20°C.

Extracted from:
Development of marine microbial community during phytoplankton detritus degradation

K. Kunnis, 1997
EMHI Marine Department, Liivalaia St. 9, Tallinn EE0106, Estonia

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**mesocosm** · 02-11-2006, 09:12 AM

Greetings All !

Bacteria have the capacity to produce and "move" polyunsaturated fatty acids (PUFA) ... eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) ... in the "food webs" of captive marine ecosystems ...

A total of 304 bacterial strains, isolated from surface sterilised amphipods, copepods, mussels and shrimps and from the intestines of freshwater and marine fish in a high-arctic region, were screened for polyunsaturated fatty acid (PUFA) producing ability. Out of 97 PUFA positive strains, 58 produced eicosapentaenoic acid (EPA) and 39 produced docosahexaenoic acid (DHA). The proportions of PUFA to total fatty acids ranged from 4% to 18% in the EPA producers and from 4% to 14% in the DHA producers when cultured at 12 C. PUFA producers were found in one out of four investigated fish species, and in all out of ten invertebrate species. EPA-producing bacteria were isolated from all invertebrates, whereas five contained additional DHA-producers. Highest abundence were found in Chlamys islandica, Gammarus wilkinson, and Astarte sp., with 77, 62 and 56% of the tested strains, respectively. On the basis of their fatty acid profiles, the PUFA-producing bacteria could be divided into nine distict groups. Group 1 to 3, tentatively classified as Pseudomonas-type of bacteria, possessed complex mixtures of even-numbered, odd-numbered and branched fatty acids, whereas group 4 to 9, being classified as Vibrio spp., were dominated by the common even-numbered fatty acid residues.

Extracted from:
Prevalence of polyunsaturated fatty acid (PUFA) producing bacteria among marine invertebrates from the Arctic.

Jøstensen, J-P. and Landfald, B., 1997
The Norwegian College of Fishery Science, University of Tromsø, N-9037 Tromsø, Norway.

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**mesocosm** · 02-11-2006, 09:24 AM

Greetings All !

There can be important differences in the enzymatic properties of "attached vs. free-living" bacteria ...

To improve our understanding on the role of bacteria in the formation and degradation of marine snow, there is a need to know what kind of organisms are present in the active community, how they are distributed in time and space and what are their ecological functions. This study is part of a larger program (PALOMA) investigating the mechanisms of the formation and degradation of large aggregates in the Northern Adriatic Sea (Golf of Trieste, Italy). We have applied molecular techniques to identify culturable heterotrophic cells isolated from macroaggregate-associated vs free-living bacterial communities and investigated the phenotypic (enzymatic activities) and phylogenetic characteristics of isolated cells. The results clearly indicate that the numbers of total and culturable bacteria do not change in space and time while important changes in the community structure were observed. The phylogenetic affiliation of 27 isolated strains show that most of free-living and attached bacteria are distributed into a and y-subclasses of proteobacteria. Some isolates are very closed to those identified in Pacific and Atlantic communities. The counts of cells which hybridized with eubacterial fluorescent multiple probes were not significantly higher than those of culturable cells indicating that the isolated cells were representative of significant part of the active community. The enzymatic properties of the isolated strains show an important heterogeneity and specificity between attached vs free-living bacteria. The capacity of each isolate to produce extracellular polysaccharides has been investigated under stressful conditions.

Extracted from:
Diversity of culturable heterotrophic bacterial communities as affected by mucilaginous aggregates formation in the North Adriatic Sea.

Céline Fajon, Jean-Francois Ghiglione, Philippe Lebaron, 1997
Observatoire Océanologique, Université Pierre et Marie Curie, Institut National des Sciences de l'Univers, URA 2071, BP44, 66651 Banyuls-sur-Mer Cedex, France

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