Lake Pavin History, geology, biogeochemistry, and sedimentology of a deep meromictic maar lake

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16.3.3.7 Top-Down Regulations: Impact
of Virus
The impact of viruses on methanogens and then on MPRs is
potentially of importance but remains completely over-
looked. Whereas viruses infecting some mesophilic and ther-
mophilic methanogens have been isolated since 20 years,
their involvement in the regulation of this key functional
group has not yet been established. The available data
(mainly on viruses of thermophilic methanogens), suggest
that these viruses belong to Caudovirales. Unlike other
archaeal viruses, the viruses of methanogens seem predomi-
nantly lytic and therefore could have a significant impact in
the regulation of methanogenic communities.
The first study, conducted a few years ago with Lake
Pavin sediments, revealed that viruses are abundant and
exhibit unexpected phenotypes. Among those phenotypes,

we detected viruses that exhibit shapes similar to known

archaeal viruses (Borrel et al. 2012c). A filamentous pro-

karyote infected with ellipsoid pleomorphic viruses was also

observed (Fig. 16.1c). The infected hosts exhibited sheath

and flat ends, similar to those observed with the cultured

archaeal methanogenic species Methanosaeta concilii (Patel

and Sprott 1990 ). Although there is no certitude about the

identity of the infected cell from Lake Pavin sediments, its

tentative affiliation to Methanosaeta was based on morpho-

logical similarities and on the predominance of members of

this archaeal group in Lake Pavin (Lehours et al. 2007 :

Borrel et al. 2012a). To further investigate the role of viruses

in the regulation of methanogenic communities (e.g., by

determining the number of infected cells), we currently

develop an approach coupling magneto-FISH and electron

microscopy (Box 16.3).

Box 16.3: The Magneto-Fish Method^11 : Does It Allow the

Study of Viral Infection of Targeted Groups of Micro-

Organisms (e.g., Methanogens)?

Magneto-FISH allows physical separation of microorgan-

isms of interest from environmental samples. This method

is based on 16S rRNA catalyzed reporter deposition

(CARD)–FISH (identity) (Pernthaler et al. 2002 ) and

immunomagnetic bead capture (separation) (Pernthaler

et al. 2008 ; Pernthaler and Orphan 2010 ). Magneto-FISH

was applied to study interspecies partnerships between

anaerobic methane-oxidizing (ANME) Archaea and sul-

fate-reducing Deltaproteobacteria (SRB) in anoxic marine

sediments (Pernthaler et al. 2008 ) illustrating that this

method is adapted for complex environmental samples.

(^11) For a detailed protocol see Trembath-Reichert et al. ( 2013 )
*TEM picture J. Colombet
** CLSM picture O. Bardot.
(continued)
16 Methanogens and Methanotrophs in Lake Pavin
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