Pierre E. Galand

Small thaw ponds: an unaccounted source of methane in the Canadian high Arctic.

Thawing permafrost in the Canadian Arctic tundra leads to peat erosion and slumping in narrow and shallow runnel ponds that surround more commonly studied polygonal ponds. Here we compared the methane production between runnel and polygonal ponds using stable isotope ratios, ¹⁴C signatures, and investigated potential methanogenic communities through high-throughput sequencing archaeal 16S rRNA genes. We found that runnel ponds had significantly higher methane and carbon dioxide emissions, produced from a slightly larger fraction of old carbon, compared to polygonal ponds. The methane stable isotopic signature indicated production through acetoclastic methanogenesis, but gene signatures from acetoclastic and hydrogenotrophic methanogenic Archaea were detected in both polygonal and runnel ponds. We conclude that runnel ponds represent a source of methane from potentially older C, and that they contain methanogenic communities able to use diverse sources of carbon, increasing the risk of augmented methane release under a warmer climate.

Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota

Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster‐V (RC‐V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC‐V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene‐based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.

Removing environmental sources of variation to gain insight on symbionts vs. transient microbes in high and low microbial abundance sponges

In this study, we pursue unravelling the bacterial communities of 26 sponges, belonging to several taxonomical orders, and comprising low microbial abundance (LMA) and high microbial abundance (HMA) representatives. Particularly, we searched for species-specific bacteria, which could be considered as symbionts. To reduce temporal and spatial environmentally caused differences between host species, we sampled all the sponge species present in an isolated small rocky area in a single dive. The bacterial communities identified by pyrosequencing the 16S rRNA gene showed that all HMA species clustered separated from LMA sponges and seawater. HMA sponges often had highest diversity, but some LMA sponges had also very diverse bacterial communities. Network analyses indicated that no core bacterial community seemed to exist for the studied sponges, not even for such a space and time-restricted sampling. Most sequences, particularly the most abundant ones in each species, were species-specific for both HMA and LMA sponges. The bacterial sequences retrieved from LMA sponges, despite being phylogenetically more similar to seawater, did not represent transient seawater bacteria. We conclude that sponge bacterial communities depend more on the host affiliation to the HMA or LMA groups than on host phylogeny.

Sulfide production and consumption in degrading wood in the marine environment

Woody debris is known to be transported to the seas and accumulate on the seafloor, however, little is known on the consequences of its degradation in the marine environment. In this study we monitored the degradation product sulfide with Au/Hg voltammetric microelectrodes on the surface and interior of an experimentally immersed wood for 200 d. After 5 weeks of immersion, the interior became sulfidic, and steady-state conditions were established after 13 weeks with sulfide concentration reaching about 300 μM. Although sulfide was briefly detected at the surface of wood, its concentration remained lower than 20 μM, indicating that this compound was effectively oxidized within the substrate. Fitting these data to a kinetic model lead to an estimated microbial sulfide production rate in the range of 19-28 μM d(-1) at steady state. As much as 24 μM d(-1) nitrate could be consumed by this process in the steady-state period. Before the establishment of the steady state conditions, steep fluctuations in sulfide concentration (between 1mM and several μM) were observed in the wood interior. This study is the first to document the temporal dynamics of this unsteady process, characterized by fast sulfide fluctuation and consumption. Our results point to the complex mechanisms driving the dynamics of wood biogeochemical transformations, and reveal the capacity of woody debris to generate sulfidic conditions and act as a possible sink for oxygen and nitrate in the marine environment.

Sunken woods on the ocean floor provide diverse specialized habitats for microorganisms.

Marine waterlogged woods on the ocean floor provide the foundation for an ecosystem resulting in high biomass and potentially high macrofaunal diversity, similarly to other large organic falls. However, the microorganisms forming the base of wood fall ecosystems remain poorly known. To study the microbial diversity and community structure of sunken woods, we analyzed over 2800 cloned archaeal and bacterial 16S rRNA gene sequences from samples with different geographic locations, depths, and immersion times. The microbial communities from different wood falls were diverse, suggesting that sunken woods provide wide-ranging niches for microorganisms. Microorganisms dwelling at sunken woods change with time of immersion most likely due to a change in chemistry of the wood. We demonstrate, for the first time in sunken woods, the co-occurrence of free-living sulfate-reducing bacteria and methanogens and the presence of sulfide oxidizers. These microorganisms were similar to those of other anaerobic chemoautotrophic environments suggesting that large organic falls can provide similar reduced habitats. Furthermore, quantification of phylogenetic patterns of microbial community assembly indicated that environmental forces (habitat filtering) determined sunken wood microbial community structure at all degradation phases of marine woodfalls. We also include a detailed discussion on novel archaeal and bacterial phylotypes in this newly explored biohabitat.

Picoplankton diversity in the Arctic Ocean and surrounding seas

Microbes, which are organisms that are visible only with a microscope, drive global biogeochemical cycling and CO2-fixing forms are the base of the marine arctic food web. Two of the three domains of life, Bacteria and Archaea, are exclusively microbial, and microbes account for the majority of diversity within the third domain, Eucarya. Although morphological diversity among the smallest microbes is limited, phylogenetic diversity among microbes is vast. With each of several major technological advances, estimates of global microbial diversity increase by orders of magnitude. The Arctic is no exception, with most major groups of marine microbes having been found in arctic marine waters using molecular biological techniques. Here we provide a brief overview of microbial diversity revealed by environmental surveys of the small subunit rRNA gene (SS rRNA), which is the most widely used marker for identifying microbes. Similar to larger phytoplankton identified morphologically, small heterotrophic prokaryotes and photosynthetic eukaryotes in the Arctic are a mixture of uniquely arctic taxa and more cosmopolitan species. Among Bacteria, Proteobacteria are predominant in surface and deep waters as with other oceans. However, the recent massively parallel sequencing of the SS rRNA gene has revealed that at finer taxonomic scales arctic bacterial and archaeal communities also differ from their temperate counterparts, suggesting endemicity as well.

Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes

Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.

Microbial communities in sunken wood are structured by wood-boring bivalves and location in a submarine canyon.

The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of Xylophaga, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of Xylophaga spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that Xylophaga spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of Xylophaga spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life.

Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific)

The Clipperton lagoon in the North Pacific Ocean has been isolated from the surrounding sea for c. 160 years. It has a stratified water column that comprises an oxic and brackish upper water layer (mixolimnion) and a deep sulfuric anoxic saline layer (monimolimnion), separated by a steep pycnocline. Here, we test whether the Clipperton lagoon with its distinctive physico-chemical features, geographic isolation, recent water column stratification, and large nutrient input harbors original microbial communities. The combination of capillary electrophoresis single-strand polymorphism (CE-SSCP) fingerprinting and sequencing of cloned bacterial and archaeal 16S rRNA genes, and functional genes for methanogenesis (mcrA), methanotrophy (pmoA), and sulfate reduction (dsrAB), revealed that microbial communities and pathways were highly stratified down the water column. The mixolimnion contained ubiquitous freshwater clades of Alpha- and Betaproteobacteria, while the pycnocline contained mostly green sulfur bacteria (phylum Chlorobi). Sequences of the upper layers were closely related to sequences found in other aquatic ecosystems, suggesting that they have a strong potential for dispersal and colonization. In contrast, the monimolimnion contained new deeply branching bacterial divisions within the OP11 cluster and the Bacteroidetes, and was the most diverse of the layers. The unique environmental conditions characterizing the deep layers of the lagoon may explain the novelty of the microbial communities found at the Clipperton atoll.

Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord

Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.