Sonja K. Fagervold

Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time<5 h). We propose a conceptual framework in which physical mixing of the water column periodically resets SAR11 communities to a high diversity state and the seasonal evolution of phosphate limitation competitively excludes deeper-dwelling ecotypes to promote low diversity states dominated (>80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study.

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.

River organic matter shapes microbial communities in the sediment of the Rhône prodelta

Microbial-driven organic matter (OM) degradation is a cornerstone of benthic community functioning, but little is known about the relation between OM and community composition. Here we use Rhône prodelta sediments to test the hypothesis that OM quality and source are fundamental structuring factors for bacterial communities in benthic environments. Sampling was performed on four occasions corresponding to contrasting river-flow regimes, and bacterial communities from seven different depths were analyzed by pyrosequencing of 16S rRNA gene amplicons. The sediment matrix was characterized using over 20 environmental variables including bulk parameters (for example, total nitrogen, carbon, OM, porosity and particle size), as well as parameters describing the OM quality and source (for example, pigments, total lipids and amino acids and δ13C), and molecular-level biomarkers like fatty acids. Our results show that the variance of the microbial community was best explained by δ13C values, indicative of the OM source, and the proportion of saturated or polyunsaturated fatty acids, describing OM lability. These parameters were traced back to seasonal differences in the river flow, delivering OM of different quality and origin, and were directly associated with several frequent bacterial operational taxonomic units. However, the contextual parameters, which explained at most 17% of the variance, were not always the key for understanding the community assembly. Co-occurrence and phylogenetic diversity analysis indicated that bacteria–bacteria interactions were also significant. In conclusion, the drivers structuring the microbial community changed with time but remain closely linked with the river OM input.

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.

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.

Disturbance Increases Microbial Community Diversity and Production in Marine Sediments

Disturbance strongly impacts patterns of community diversity, yet the shape of the diversity-disturbance relationship remains a matter of debate. The topic has been of interest in theoretical ecology for decades as it has practical implications for the understanding of ecosystem services in nature. One of these processes is the remineralization of organic matter by microorganisms in coastal marine sediments, which are periodically impacted by disturbances across the sediment-water interface. Here we set up an experiment to test the hypothesis that disturbance impacts microbial diversity and function during the anaerobic degradation of organic matter in coastal sediments. We show that during the first 3 weeks of the experiment, disturbance increased both microbial production, derived from the increase in microbial abundance, and diversity of the active fraction of the community. Both community diversity and phylogenetic diversity increased, which suggests that disturbance promoted the cohabitation of ecologically different microorganisms. Metagenome analysis also showed that disturbance increased the relative abundance of genes diagnostic of metabolism associated with the sequential anaerobic degradation of organic matter. However, community composition was not impacted in a systematic way and changed over time. In nature, we can hypothesize that moderate storm disturbances, which impact coastal sediments, promote diverse, and productive communities. These events, rather than altering the decomposition of organic matter, may increase the substrate turnover and, ultimately, remineralization rates.

DIVERSITY OF BACTERIAL COMMUNITIES ON SUNKEN WOODS IN THE MEDITERRANEAN SEA

Sunken woods are very rich and diverse ecosystems supporting large macrofaunal diversity and representing a source of carbon and energy for any heterotrophic organism able to consume plant material, and those relying on specialized microbial taxa. However, relatively little is known about the microbial communities that degrade sunken woods and produce reduced compounds that serve as energy sources for chemosynthetic lifestyles. The purpose of this study was to explore the bacterial diversity developing on and within sunken woods in a NW Mediterranean submarine canyon and its adjacent slope by using 16S rRNA genes survey. We described communities from Pine wood immerged at 1200m deep in the Blanes Canyon and its adjacent open slope, as well as from material filling wood boring bivalve burrows. We demonstrate that bacterial communities were very different from each other in each of the three wood ecosystems. These highly diverse wood communities contained all the major bacterial phyla, but Alphaproteobacteria and Deltaproteobacteria were dominant in the open slope and the canyon, respectively. The burrows had more Gamma- and Epsilon-proteobacteria. In summary, highly diverse bacterial communities with potentially wide metabolic capabilities colonized wood sunken in the Blanes Canyon and its adjacent open slopes in the Mediterranean Sea.

Pleionea mediterranea gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater.

A Gram-negative, aerobic, cream-pigmented, non-motile, non-spore-forming straight rod, strain MOLA115(T), was isolated from a coastal water sample from the Mediterranean Sea. On the basis of phylogenetic analysis of the 16S rRNA gene sequences, strain MOLA115(T) was shown to belong to the Gammaproteobacteria, adjacent to members of the genera Marinicella, Arenicella and Kangiella, sharing less than 89 % 16S rRNA gene sequence similarity with strains of all recognized species within the Gammaproteobacteria. The only isoprenoid quinone was ubiquinone-8. Polar lipids in strain MOLA115(T) included phosphatidylethanolamine, an aminolipid, phosphatidylglycerol and an aminophospholipid. Fatty acid analysis revealed iso-C15 : 0 and iso-C17 : 1ω9c to be the dominant components. The DNA G+C content was 44.5 mol%. Based upon the phenotypic and phylogenetic data, we propose that strain MOLA115(T) should be considered to represent a novel species in a new genus, for which the name Pleionea mediterranea gen. nov., sp. nov. is proposed. The type strain of Pleionea mediterranea is MOLA115(T) ( = CIP 110343(T) = DSM 25350(T)).

Saonia flava gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from coastal seawater

A Gram-stain-negative, aerobic, yellow-pigmented, straight rod-shaped bacterium, strain MOLA117T, was isolated from a coastal water sample from the north-western Mediterranean Sea, near Banyuls-sur-Mer, France. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, strain MOLA117T was placed within the family Flavobacteriaceae, but showed less than 93 % 16S rRNA gene sequence similarity to other recognized species within the family. The most closely related genera included Arenibacter, Cellulophaga, Maribacter and Zobellia. The only isoprenoid quinone was menaquinone MK-6 and the predominant fatty acid was iso-C17 : 0 3-OH, representing over 33 % of the total fatty acids. The DNA G+C content was 36.9 mol%. Strain MOLA117T required NaCl for growth, and did not exhibit gliding motility or produce flexirubin. Based on the phenotypic and phylogenetic data, strain MOLA117T should be considered to represent a novel species of a new genus, for which the name Saonia flava gen. nov., sp. nov. is proposed. The type strain of Saonia flava is MOLA117T (=CIP 110873T=DSM 29762T).