References
Ackermann H-W (2003) Bacteriophage observations and evolution.
Res Microbiol 154:245–251
Aller RC, Aller JY (1992) Meiofauna and solute transport in marine
muds. Limnol Oceanogr 37:1018–1033
Amblard C, Carrias JF, Bourdier G, Maurin N (1995) The microbial
loop in a humic lake: seasonal and vertical variations in the structure
of the different communities. Hydrobiologia 300(301):71–84
Amblard C, Boisson JC, Bourdier G, Fontvieille D, Gayte X, SimeNgando T (1998) Ecologie microbienne en milieu aquatique: des
virus aux protozoaires. Rev Sc. Eau, N
Spe ´cial: Les Sciences de
l’Eau: Bilan et perspectives, 145–162
Anderson JM (2000) Food web functioning and ecosystem processes.
In: Colemab DC, Hendrix PF (eds) Invertebrates as webmasters in
ecosystems. CABI Publishing, Wallunford, pp 3–24
Angly FE et al (2006) The marine viromes of four oceanic regions.
PLoS Biol 4:e368
Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F
(1983) The ecological role of water-column microbes in the sea.
Mar Ecol Prog Ser 10:257–263
Badejo MA, Tian G (1999) Abundance of soil mites under four agroforestry tree species with contrasting litter quality. Biol Fertil Soils
30:107–112
Bardgett RD (2005a) Organism interactions and soil processes. In:
Crawley MJ, Little C, Southwood TRE, Ulfstrand S (eds) The
biology of soil, a community and ecosystem approach. Oxford
University Press, Oxford, UK, pp 57–85
Bardgett RD (2005b) The diversity of life in soil. In: Crawley MJ, Little
C, Southwood TRE, Ulfstrand S (eds) The biology of soil, a community and ecosystem approach. Oxford University Press, Oxford,
UK, pp 24–56
Beare MH, Coleman DC, Crossley DA, Hendrix PF, Odum EP (1995)
A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant and Soil 170:5–22
Bec A, Martin-Creuzburg D, von Elert E (2006) Trophic upgrading of
autotrophic picoplankton by the heterotrophic nanoflagellate
Paraphysomonas sp. Limnol Oceanogr 51:1699–1707
Bergh O, Børsheim KY, Bratbak G, Heldal M (1989) High abundance
of viruses found in aquatic environments. Nature 340:467–468
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere
the same virus? Trends Microbiol 13:278–284
Brown GG (1995) How do earthworms affect microfloral and faunal
community diversity. Plant and Soil 170:209–231
Buffan-Dubau E, Carman KR (2000) Diel feeding behavior of
meiofauna and their relationships with microalgal resources.
Limnol Oceanogr 45:381–395
Carpenter SR (1988) Complex interactions in lake communities.
Springer, New York
Carrias JF, Amblard C, Bourdier G (1998) Seasonal dynamics and
vertical distribution of planktonic ciliates and their relationship to
microbial food resources in the oligomesotrophic lake Pavin. Arch
Hydrobiol 143:227–255
Colombet J (2008) Importance de la variabilite ´ verticale dans un lac
me ´romictique profond: diversite ´ et activite ´ lysoge `ne des
communaute ´s virales. The `se de Doctorat, Universite ´ Blaise Pascal,
204 p
Curtis TP, Sloan WT, Scannel JW (2002) Estimating prokaryotic
diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499
Cushing DH (1989) A difference in structure between ecosystems in
strongly stratified waters and in those that are only weakly stratified.
J Plank Res 11:1–13
De Ruiter PC, Neutel AN, Moore JC (1995) Energetics, patterns of
interactions strengths and stability in real ecosystems. Science
269:1257–1260
De Ruiter PC, Neutel AN, Moore JC (1997) Soil foodweb interactions
and modelling. In: Benckiser G (ed) Fauna in soil ecosystems.
Dekker, New York, pp 363–386
Degens B, Harris JA (2000) Decreases in organic C reserves in soil can
reduce the catabolic diversity of soil microbial communities. Soil
Biol Biochem 32:189–196
Delong EF (1992) Archaea in coastal marine environments. Proc Natl
Acad Sci U S A 89:5685–5689
Dolan JR (1997) Phosphorus and ammonia excretion by planktonic
protists. Mar Geol 139:109–122
Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev
Microbiol 3:504–510
Egerton-Warburton L, Allen EB (2000) Shifts in arbuscular mycorrhizal communities along an anthropogenic nitrogen deposition gradient. Ecol Appl 10:484–496
Filippini M, Buesing N, Bettarel Y, Sime-Ngando T, Gessner MO
(2006) Infection paradox: high abundance but low impact of freshwater benthic viruses. Appl Environ Microbiol 72:4893–4898
Foissner W (1997a) Global soil ciliate (Protozoa: Ciliophora) diversity:
a probability-based approach using large sample collections from
Africa, Australia and Antarctica. Biodivers Conserv 5:1627–1638
Foissner W (1997b) Soil ciliates (Protozoa: Ciliophora) from evergreen
rain forest of Australia, South America and Costa Rica: diversity
and description of new species. Biol Fertil Soils 25:317–339
Forterre P (2007) Microbes de l’enfer. Edition Belin, Paris
Fouilland E, Mostajir B (2010) Revisited phytoplanktonic carbon
dependency of heterotrophic bacteria in freshwater, transitional,
coastal and oceanic waters. FEMS Microbiol Ecol 73:419–429
Fouilland E, Mostajir B (2011) Complementary support for the new
ecological concept of “bacterial independence on contemporary
phytoplankton production” in oceanic Waters. FEMS Microbiol
Ecol 78:206–209
Fouilland E, Gosselin M, Rivkin RB, Vasseur C, Mostajir B (2007)
Nitrogen uptake by heterotrophic bacteria and phytoplankton in
Arctic surface waters. J Plankton Res 29:369–376
Fuhrman JA (1999) Marine viruses and their biogeochemical and
ecological effects. Nature 399:541–548
Giere O (2009) Meiobenthology: the microscopic motile fauna of
aquatic sediments. Springer, Berlin/Heidelberg
Grami B, Rasconi S, Niquil N, Jobard M, Saint-Be ´at B, Sime-Ngando T
(2011) Functional effects of parasites on food web properties during
the spring diatom bloom in Lake Pavin: a linear inverse modeling
analysis. PLoS One 6:e23273
Hedlund K, Boddy L, Preston CM (1991) Mycelial response of the soil
fungus, Mortierella Isabellina, to grazing by Onychiurus armatus
(collembolan). Soil Biol Biochem 23:361–366
Hobbie JE, Daley RJ, Jasper S (1977) Use of Nuclepore filters for
counting bacteria by fluorescence microscopy. Appl Environ
Microbiol 33:1225–1228
Jardillier L, Boucher D, Personnic S, Jacquet S, Thenot A, Sargos D,
Amblard C, Debroas D (2005) Relative importance of nutrients and
mortality factors on prokaryotic community composition in two
lakes of different trophic status: microcosm experiments. FEMS
Microbiol Ecol 53:429–443
Kagami M, De Bruin A, Ibelings BW, Van Donk E (2007) Parasitic
chytrids: their effects on phytoplankton communities and food-web
dynamics. Hydrobiologia 578:113–129
Kolber ZS, Van Dover CL, Niederman RA, Falkowski PG (2000)
Bacterial photosynthesis in surface waters of the open ocean. Nature
407:177–179
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
507
Ackermann H-W (2003) Bacteriophage observations and evolution.
Res Microbiol 154:245–251
Aller RC, Aller JY (1992) Meiofauna and solute transport in marine
muds. Limnol Oceanogr 37:1018–1033
Amblard C, Carrias JF, Bourdier G, Maurin N (1995) The microbial
loop in a humic lake: seasonal and vertical variations in the structure
of the different communities. Hydrobiologia 300(301):71–84
Amblard C, Boisson JC, Bourdier G, Fontvieille D, Gayte X, SimeNgando T (1998) Ecologie microbienne en milieu aquatique: des
virus aux protozoaires. Rev Sc. Eau, N
Spe ´cial: Les Sciences de
l’Eau: Bilan et perspectives, 145–162
Anderson JM (2000) Food web functioning and ecosystem processes.
In: Colemab DC, Hendrix PF (eds) Invertebrates as webmasters in
ecosystems. CABI Publishing, Wallunford, pp 3–24
Angly FE et al (2006) The marine viromes of four oceanic regions.
PLoS Biol 4:e368
Azam F, Fenchel T, Field JG, Gray JS, Meyer-Reil LA, Thingstad F
(1983) The ecological role of water-column microbes in the sea.
Mar Ecol Prog Ser 10:257–263
Badejo MA, Tian G (1999) Abundance of soil mites under four agroforestry tree species with contrasting litter quality. Biol Fertil Soils
30:107–112
Bardgett RD (2005a) Organism interactions and soil processes. In:
Crawley MJ, Little C, Southwood TRE, Ulfstrand S (eds) The
biology of soil, a community and ecosystem approach. Oxford
University Press, Oxford, UK, pp 57–85
Bardgett RD (2005b) The diversity of life in soil. In: Crawley MJ, Little
C, Southwood TRE, Ulfstrand S (eds) The biology of soil, a community and ecosystem approach. Oxford University Press, Oxford,
UK, pp 24–56
Beare MH, Coleman DC, Crossley DA, Hendrix PF, Odum EP (1995)
A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant and Soil 170:5–22
Bec A, Martin-Creuzburg D, von Elert E (2006) Trophic upgrading of
autotrophic picoplankton by the heterotrophic nanoflagellate
Paraphysomonas sp. Limnol Oceanogr 51:1699–1707
Bergh O, Børsheim KY, Bratbak G, Heldal M (1989) High abundance
of viruses found in aquatic environments. Nature 340:467–468
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere
the same virus? Trends Microbiol 13:278–284
Brown GG (1995) How do earthworms affect microfloral and faunal
community diversity. Plant and Soil 170:209–231
Buffan-Dubau E, Carman KR (2000) Diel feeding behavior of
meiofauna and their relationships with microalgal resources.
Limnol Oceanogr 45:381–395
Carpenter SR (1988) Complex interactions in lake communities.
Springer, New York
Carrias JF, Amblard C, Bourdier G (1998) Seasonal dynamics and
vertical distribution of planktonic ciliates and their relationship to
microbial food resources in the oligomesotrophic lake Pavin. Arch
Hydrobiol 143:227–255
Colombet J (2008) Importance de la variabilite ´ verticale dans un lac
me ´romictique profond: diversite ´ et activite ´ lysoge `ne des
communaute ´s virales. The `se de Doctorat, Universite ´ Blaise Pascal,
204 p
Curtis TP, Sloan WT, Scannel JW (2002) Estimating prokaryotic
diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499
Cushing DH (1989) A difference in structure between ecosystems in
strongly stratified waters and in those that are only weakly stratified.
J Plank Res 11:1–13
De Ruiter PC, Neutel AN, Moore JC (1995) Energetics, patterns of
interactions strengths and stability in real ecosystems. Science
269:1257–1260
De Ruiter PC, Neutel AN, Moore JC (1997) Soil foodweb interactions
and modelling. In: Benckiser G (ed) Fauna in soil ecosystems.
Dekker, New York, pp 363–386
Degens B, Harris JA (2000) Decreases in organic C reserves in soil can
reduce the catabolic diversity of soil microbial communities. Soil
Biol Biochem 32:189–196
Delong EF (1992) Archaea in coastal marine environments. Proc Natl
Acad Sci U S A 89:5685–5689
Dolan JR (1997) Phosphorus and ammonia excretion by planktonic
protists. Mar Geol 139:109–122
Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev
Microbiol 3:504–510
Egerton-Warburton L, Allen EB (2000) Shifts in arbuscular mycorrhizal communities along an anthropogenic nitrogen deposition gradient. Ecol Appl 10:484–496
Filippini M, Buesing N, Bettarel Y, Sime-Ngando T, Gessner MO
(2006) Infection paradox: high abundance but low impact of freshwater benthic viruses. Appl Environ Microbiol 72:4893–4898
Foissner W (1997a) Global soil ciliate (Protozoa: Ciliophora) diversity:
a probability-based approach using large sample collections from
Africa, Australia and Antarctica. Biodivers Conserv 5:1627–1638
Foissner W (1997b) Soil ciliates (Protozoa: Ciliophora) from evergreen
rain forest of Australia, South America and Costa Rica: diversity
and description of new species. Biol Fertil Soils 25:317–339
Forterre P (2007) Microbes de l’enfer. Edition Belin, Paris
Fouilland E, Mostajir B (2010) Revisited phytoplanktonic carbon
dependency of heterotrophic bacteria in freshwater, transitional,
coastal and oceanic waters. FEMS Microbiol Ecol 73:419–429
Fouilland E, Mostajir B (2011) Complementary support for the new
ecological concept of “bacterial independence on contemporary
phytoplankton production” in oceanic Waters. FEMS Microbiol
Ecol 78:206–209
Fouilland E, Gosselin M, Rivkin RB, Vasseur C, Mostajir B (2007)
Nitrogen uptake by heterotrophic bacteria and phytoplankton in
Arctic surface waters. J Plankton Res 29:369–376
Fuhrman JA (1999) Marine viruses and their biogeochemical and
ecological effects. Nature 399:541–548
Giere O (2009) Meiobenthology: the microscopic motile fauna of
aquatic sediments. Springer, Berlin/Heidelberg
Grami B, Rasconi S, Niquil N, Jobard M, Saint-Be ´at B, Sime-Ngando T
(2011) Functional effects of parasites on food web properties during
the spring diatom bloom in Lake Pavin: a linear inverse modeling
analysis. PLoS One 6:e23273
Hedlund K, Boddy L, Preston CM (1991) Mycelial response of the soil
fungus, Mortierella Isabellina, to grazing by Onychiurus armatus
(collembolan). Soil Biol Biochem 23:361–366
Hobbie JE, Daley RJ, Jasper S (1977) Use of Nuclepore filters for
counting bacteria by fluorescence microscopy. Appl Environ
Microbiol 33:1225–1228
Jardillier L, Boucher D, Personnic S, Jacquet S, Thenot A, Sargos D,
Amblard C, Debroas D (2005) Relative importance of nutrients and
mortality factors on prokaryotic community composition in two
lakes of different trophic status: microcosm experiments. FEMS
Microbiol Ecol 53:429–443
Kagami M, De Bruin A, Ibelings BW, Van Donk E (2007) Parasitic
chytrids: their effects on phytoplankton communities and food-web
dynamics. Hydrobiologia 578:113–129
Kolber ZS, Van Dover CL, Niederman RA, Falkowski PG (2000)
Bacterial photosynthesis in surface waters of the open ocean. Nature
407:177–179
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
507