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Abstract:
Temperature is an important factor regulating the production of the
greenhouse gas CH4. Structure and function of the methanogenic microbial
communities are often drastically different upon incubation at 45
degrees C versus 25 degrees C or 35 degrees C, but are also different in
different soils. However, the extent of taxonomic redundancy within each
functional group and the existence of different temperature-dependent
microbial community network modules are unknown. Therefore, we
investigated paddy soils from Italy and the Philippines and a desert
soil from Utah (United States), which all expressed CH4 production upon
flooding and exhibited structural and functional differences upon
incubation at three different temperatures. We continued incubation of
the pre-incubated soils (Liu et al., 2018) by changing the temperature
in a factorial manner. We determined composition, abundance and function
of the methanogenic archaeal and bacterial communities using HiSeq
Illumine sequencing, qPCR and analysis of activity and stable isotope
fractionation, respectively. Heatmap analysis of operational taxonomic
units (OTU) from the different incubations gave detailed insights into
the community structures and their putative functions. Network analysis
showed that the microbial communities in the different soils were all
organized within modules distinct for the three incubation temperatures.
The diversity of Bacteria and Archaea was always lower at 45 degrees C
than at 25 or 35 degrees C. A shift from 45 degrees C to lower
temperatures did not recover archaeal diversity, but nevertheless
resulted in the establishment of structures and functions that were
largely typical for soil at moderate temperatures. At 25 and 35 degrees
C and after shifting to one of these temperatures, CH4 was always
produced by a combination of acetoclastic and hydrogenotrophic
methanogenesis being consistent with the presence of acetoclastic
(Methanosarcinaceae, Methanotrichaceae) and hydrogenotrophic
(Methanobacteriales, Methanocellales, Methanosarcinaceae) methanogens.
At 45 degrees C, however, or after shifting from moderate temperatures
to 45 degrees C, only the Philippines soil maintained such combination,
while the other soils were devoid of acetoclastic methanogens and
consumed acetate instead by syntrophic acetate oxidation coupled to
hydrogenotrophic methanogenesis. Syntrophic acetate oxidation was
apparently achieved by Thermoanaerobacteraceae, which were especially
abundant in Italian paddy soil and Utah desert soil when incubated at 45
degrees C. Other bacterial taxa were also differently abundant at 45
degrees C versus moderate temperatures, as seen by the formation of
specific network modules. However, the archaeal OTUs with putative
function in acetoclastic or hydrogenotrophic methanogenesis as well as
the bacterial OTUs were usually not identical across the different soils
and incubation conditions, and if they were, they suggested the
existence of mesophilic and thermophilic ecotypes within the same OTUs.
Overall, methanogenic function was determined by the bacterial and/or
archaeal community structures, which in turn were to quite some extent
determined by the incubation temperature, albeit largely individually in
each soil. There was quite some functional redundancy as seen by
different taxonomic community structures in the different soils and at
the different temperatures.
