Andre-Jean Francez

The Microbial Loop at the Surface of a Peatland:Structure, Function, and Impact of Nutrient Input

A bstractThe aim of this study was to assess the structure and function of the microbial loop in a peatland of the French Massif central, and the impact of fertilization on the different microbial communities.In terms of biomass, testate Amoeba (48% of the total microbial biomass), heterotrophic bacteria (15%), cyanobacteria (14%) and Bacillariophyceae (13%) were the dominant groups of microorganisms. Other microalgae (7%), ciliates (2%) and heterotrophic flagellates (1%) accounted for only a low proportion of total microbial biomass. The relative importance of heterotrophic microorganisms was higher than in marine or lacustrine environments. In addition, ciliates and heterotrophic flagellates only constituted a small proportion of the total protozoan biomass, which was heavily dominated by testate amoeba. Thus, the structure of the protist community in the subaquatic peatland was completely different from that reported for lakes or marine environments.In other aspects, the supply of nutrients (PKCa and NPKCa) resulted in increases of the relative biomasses of heterotrophic bacteria, Bacillariophyceae, and ciliates and by a decrease in the relative proportion of testate amoeba and of other microalgae.

Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands.

Exploitation of northern peatlands and biodiversity maintenance: a conflict between economy and ecology.

Peatlands are ecosystems of exceptional conservation value because of their beauty, biodiversity, importance in global geochemical cycles, and the paleoenvironmental records they preserve. Commercial extraction and drainage for forestry or agriculture have caused the destruction of many peatlands, especially in or close to urban areas of the northern temperate zone. Are these commercial and environmental interests irreconcilable? A close analysis suggests that limited peat extraction may actually increase biodiversity in some cases, and may be sustainable over the long term. As we learn more about how peatlands spontaneously regenerate following disturbance, and what conditions govern the re-establishment of a diverse community and the ability to sequester carbon, we increase our chances of being able to restore damaged peatlands. Preserving the chronological records hidden in the peat profile, the natural heritage value of peatlands, and the bulk of sequestered carbon, however, will remain incompatible with any form of exploitation.

Short-term effect of nitrogen enrichment on the microbial communities of a peatland

The aim of this study was to assess the structure of the microbial loop in a Sphagnum fallax —Carex rostrata fen of the French Massif central,and the impact of nitrogen supplies on the different microbial communities. Microalgae (46% of the total microbial biomass),Protozoa (26%) and heterotrophic Bacteria (17%) were the dominant microorganisms.Rotifera (5%),Cyanobacteria (3%),Fungi (2%) and Nematoda (< 1%) were also present.Testate Amoebae were well represented in Sphagnum peatland (14% of total microbial biomass).Thus,the structure of the protist community in the surface of fen peatlands is notably different from that recorded in other environments.The input of nitrogen led to a steady increase in microbial biomasses,but only changed the structure of microbial communities significantly when the input was 50 kg ha-1.At high inputs,nitrogen supply increased the relative importance of Cyanobacteria, Euglenophyceae, Bacillariophyceae and Ciliates, and decreased the relative importance of heterotrophic Bacteria, other microalgae and testate Amoebae. The increase in the values of photosynthetic assimilation and heterotrophic activities could also reflect changes in community functioning.

The fate of NH4NO3 added to Sphagnum magellanicum carpets at five European mire sites

Nitrogen additions as NH4NO3 corresponding to 0 (N0), 1 (N1), 3 (N3) and 10 (N10) g N m-2 yr-1 were made to Sphagnum magellanicum cores at two-week intervals in situ at four sites across Europe, i.e. Lakkasuo (Finland), Männikjärve (Estonia), Moidach More (UK) and Côte de Braveix (France). The same treatments were applied in a glasshouse experiment in Neuchâtel (Switzerland) in which the water table depth was artificially maintained at 7, 17 and 37 cm below the moss surface. In the field, N assimilation in excess of values in wet deposition occurred in the absence of growth, but varied widely between sites, being absent in Lakkasuo (moss N:P ratio 68) and greatest in Moidach More (N:P 21). In the glasshouse, growth was reduced by lowering the water table without any apparent effect on N assimilation. Total N content of the moss in field sites increased as the mean depth of water table increased indicating growth limitation leading to increased N concentrations which could reduce the capacity for N retention. Greater contents of NH4+ in the underlying peat at 30 cm depth, both in response to NH4NO3 addition and in the unamended cores confirmed poor retention of inorganic N by the moss at Lakkasuo. Nitrate contents in the profiles at Lakkasuo, Moidach More, and Côte de Braveix were extremely low, even in the N10 treatment, but in Männikjärve, where the mean depth of water table was greatest and retention absent, appreciable amounts of NO3- were detected in all cores. It is concluded that peatland drainage would reduce the capture of inorganic N in atmospheric deposition by Sphagnum mosses.

Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics

A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.

Time-scales of hydrological forcing on the geochemistry and bacterial community structure of temperate peat soils

Peatlands are an important global carbon reservoir. The continued accumulation of carbon in peatlands depends on the persistence of anoxic conditions, in part induced by water saturation, which prevents oxidation of organic matter, and slows down decomposition. Here we investigate how and over what time scales the hydrological regime impacts the geochemistry and the bacterial community structure of temperate peat soils. Peat cores from two sites having contrasting groundwater budgets were subjected to four controlled drought-rewetting cycles. Pore water geochemistry and metagenomic profiling of bacterial communities showed that frequent water table drawdown induced lower concentrations of dissolved carbon, higher concentrations of sulfate and iron and reduced bacterial richness and diversity in the peat soil and water. Short-term drought cycles (3–9 day frequency) resulted in different communities from continuously saturated environments. Furthermore, the site that has more frequently experienced water table drawdown during the last two decades presented the most striking shifts in bacterial community structure, altering biogeochemical functioning of peat soils. Our results suggest that the increase in frequency and duration of drought conditions under changing climatic conditions or water resource use can induce profound changes in bacterial communities, with potentially severe consequences for carbon storage in temperate peatlands.

Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands

Abstract A new group of viruses carrying naturally chimeric single-stranded (ss) DNA genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has been recently identified by metagenomic studies. The host range, genomic diversity, and abundance of these chimeric viruses, referred to as cruciviruses, remain largely unknown. In this article, we assembled and analyzed thirty-seven new crucivirus genomes from twelve peat viromes, representing twenty-four distinct genome organizations, and nearly tripling the number of available genomes for this group. All genomes possess the two characteristic genes encoding for the conserved capsid protein (CP) and a replication protein. Additional ORFs were conserved only in nearly identical genomes with no detectable similarity to known genes. Two cruciviruses possess putative introns in their replication-associated genes. Sequence and phylogenetic analyses of the replication proteins revealed intra-gene chimerism in at least eight chimeric genomes. This highlights the large extent of horizontal gene transfer and recombination events in the evolution of ssDNA viruses, as previously suggested. Read mapping analysis revealed that members of the ‘Cruciviridae’ group are particularly prevalent in peat viromes. Sequences matching the CP ranged from 0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine available viromes derived from other environments, only twenty-four contained cruciviruses, which on average accounted for merely 0.2 percent of sequences. Overall, this study provides new genome information and insights into the diversity of chimeric viruses, a necessary first step in progressing toward an accurate quantification and host range identification of these new viruses.

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat

Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 106 to 5.6 x 108 particles mL-1, and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands.