Methanotrophic activity and diversity of methanotrophs in volcanic geothermal soils at Pantelleria (Italy)

Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including
CH4, a greenhouse gas twenty-five times as potent as CO2.
Recently, it has been demonstrated that volcanic or geothermal soils are not only a source of methane, but are also sites
of methanotrophic activity. Methanotrophs are able to consume 10-40 Tg of CH4
a
-1
and to trap more than 50 % of the
methane degassing through the soils. We report on methane
microbial oxidation in the geothermally most active site of
Pantelleria (Italy), Favara Grande, whose total methane emission was previously estimated at about 2.5 Mg a
-1
(t a
-1
).
Laboratory incubation experiments with three top-soil samples from Favara Grande indicated methane consumption
values of up to 59.2 nmol g
-1
soil d.w. h
-1
. One of the
three sites, FAV2, where the highest oxidation rate was detected, was further analysed on a vertical soil profile, the
maximum methane consumption was measured in the topsoil layer, and values greater than 6.23 nmol g
-1
h
-1
were
still detected up to a depth of 13 cm. The highest consumption rate was measured at 37
o
C, but a still detectable
consumption at 80
o
C (> 1.25 nmol g
-1
h
-1
) was recorded.
The soil total DNA extracted from the three samples was
probed by Polymerase Chain Reaction (PCR) using standard proteobacterial primers and newly designed verrucomicrobial primers, targeting the unique methane monooxygenase gene pmoA; the presence of methanotrophs was detected
at sites FAV2 and FAV3, but not at FAV1, where harsher
chemical-physical conditions and negligible methane oxidation were detected. The pmoA gene libraries from the
most active site (FAV2) pointed to a high diversity of
gammaproteobacterial methanotrophs, distantly related to
Methylocaldum-Metylococcus genera, and the presence of
the newly discovered acido-thermophilic Verrucomicrobia
methanotrophs. Alphaproteobacteria of the genus Methylocystis were isolated from enrichment cultures under a
methane-containing atmosphere at 37
o
C. The isolates grow
at a pH range of 3.5 to 8 and temperatures of 18-45
o
C,
and consume 160 nmol of CH
4
h
-1
mL
-1
of culture. Soils
from Favara Grande showed the largest diversity of methanotrophic bacteria detected until now in a geothermal soil.
While methanotrophic Verrucomicrobia are reported as dominating highly acidic geothermal sites, our results suggest
that slightly acidic soils, in high-enthalpy geothermal systems, host a more diverse group of both culturable and uncultivated methanotrophs.