Heli Juottonen

Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire

Methane (CH4) emissions from boreal wetlands show considerable seasonal variation, including small winter emissions. We addressed the seasonality of CH4-producing microbes by comparing archaeal communities and the rates and temperature response of CH4 production in a boreal fen at three key phases of growing season and in winter. Archaeal community analysis by terminal restriction fragment length polymorphism and cloning of 16S ribosomal DNA and reverse-transcribed RNA revealed slight community shifts with season. The main archaeal groups remained the same throughout the year and were Methanosarcinaceae, Rice cluster II and Methanomicrobiales-associated Fen cluster. These methanogens and the crenarchaeal groups 1.1c and 1.3 were detected from DNA and RNA, but the family Methanosaetaceae was detected only from RNA. Differences between DNA- and RNA-based results suggested higher stability of DNA-derived communities and better representation of the active CH4 producers in RNA. Methane production potential, measured as formation of CH4 in anoxic laboratory incubations, showed prominent seasonality. The potential was strikingly highest in winter, possibly due to accumulation of methanogenic substrates, and maximal CH4 production was observed at ca. 30 °C. Archaeal community size, determined by quantitative PCR, remained similar from winter to summer. Low production potential in late summer after a water level draw-down suggested diminished activity due to oxygen exposure. Our results indicated that archaeal community composition and size in the boreal fen varied only slightly despite the large fluctuations of methanogenic potential. Detection of mRNA of the methanogenic mcrA gene confirmed activity of methanogens in winter, accounting for previously reported winter CH4 emissions.

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

Methane-cycling microbial communities and methane emission in natural and restored peatlands

ABSTRACT We addressed how restoration of forestry-drained peatlands affects CH4-cycling microbes. Despite similar community compositions, the abundance of methanogens and methanotrophs was lower in restored than in natural sites and correlated with CH4 emission. Poor establishment of methanogens may thus explain low CH4 emissions on restored peatlands even 10 to 12 years after restoration.

Archaeal rRNA diversity and methane production in deep boreal peat.

Northern peatlands play a major role in the global carbon cycle as sinks for CO(2) and as sources of CH(4). These diverse ecosystems develop through accumulation of partially decomposed plant material as peat. With increasing depth, peat becomes more and more recalcitrant due to its longer exposure to decomposing processes. Compared with surface peat, deeper peat sediments remain microbiologically poorly described. We detected active archaeal communities even in the deep bottom layers (-220/-280 cm) of two Finnish fen-type peatlands by 16S rRNA-based terminal restriction fragment length polymorphism analysis. In the sediments of the northern study site, all detected archaea were methanogens with Rice Cluster II (RC-II) and Methanosaetaceae as major groups. In southern peatland, Crenarchaeota of a rare unidentified cluster were present together with mainly RC-II methanogens. RNA profiles showed a larger archaeal diversity than DNA-based community profiles, suggesting that small but active populations were better visualized with rRNA. In addition, potential methane production measurements indicated methanogenic activity throughout the vertical peat profiles.

Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens

Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen.