Fluid flow drives phenotypic heterogeneity in bacterial growth and adhesion on surfaces.

Bacteria often thrive in surface-attached communities, where they can form biofilms affording them multiple advantages. In this sessile form, fluid flow is a key component of their environments, renewing nutrients and transporting metabolic products and signaling molecules. It also controls colonization patterns and growth rates on surfaces, through bacteria transport, attachment and detachment.

Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer.

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically.

Kinetic Study on Clogging of a Geothermal Pumping Well Triggered by Mixing-Induced Biogeochemical Reactions.

The sustainability of ground-source geothermal systems can be severely impacted by microbially mediated clogging processes. Biofouling of water wells by hydrous ferric oxide is a widespread problem. Although the mechanisms and critical environmental factors associated with clogging development are widely recognized, effects of mixing processes within the wells and time scales for clogging processes are not well characterized.

Autotrophic denitrification supported by biotite dissolution in crystalline aquifers (1): New insights from short-term batch experiments.

We investigate denitrification mechanisms through batch experiments using crushed rock and groundwater from a granitic aquifer subject to long term pumping (Ploemeur, France). Except for sterilized experiments, extensive denitrification reaction induces NO decreases ranging from 0.3 to 0.

Autotrophic denitrification supported by biotite dissolution in crystalline aquifers: (2) transient mixing and denitrification dynamic during long-term pumping.

We investigated the mixing and dynamic of denitrification processes induced by long-term pumping in the crystalline aquifer of Ploemeur (Brittany, France). Hydrological and geochemical parameters have been continuously recorded over 15 boreholes in 5km on a 25-year period. This extensive spatial and temporal monitoring of conservative as well as reactive compounds is a key opportunity to identify aquifer-scale transport and reactive processes in crystalline aquifers.

Ecophylogeny of the endospheric root fungal microbiome of co-occurring .

Background: Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce.

Methods: We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an population.

Diversity and comparative genomics of chimeric viruses in dominated peatlands.

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.

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.

Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths.

This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA.

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.

Impact of climate changes during the last 5 million years on groundwater in basement aquifers.

Climate change is thought to have major effects on groundwater resources. There is however a limited knowledge of the impacts of past climate changes such as warm or glacial periods on groundwater although marine or glacial fluids may have circulated in basements during these periods. Geochemical investigations of groundwater at shallow depth (80-400 m) in the Armorican basement (western France) revealed three major phases of evolution: (1) Mio-Pliocene transgressions led to marine water introduction in the whole rock porosity through density and then diffusion processes, (2) intensive and rapid recharge after the glacial maximum down to several hundred meters depths, (3) a present-day regime of groundwater circulation limited to shallow depth.

Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands.

Microviridae, a family of bacteria-infecting ssDNA viruses, is one of the still poorly characterized bacteriophage groups, even though it includes phage PhiX174, one of the main models in virology for genomic and capsid structure studies. Recent studies suggest that they are diverse and well represented in marine and freshwater virioplankton as well as in human microbiomes. However, their diversity, abundance, and ecological role are completely unknown in soil ecosystems.

The importance of the microbiome of the plant holobiont.

Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses.

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.

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin.

The subsurface realm is colonized by microbial communities to depths of >1000 meters below the seafloor (m.b.sf.

PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

Background: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases.

Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics.

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses.

Function and evolution of the psbA gene family in marine Synechococcus: Synechococcus sp. WH7803 as a case study.

In cyanobacteria, the D1 protein of photosystem II (PSII) is encoded by the psbA multigene family. In most freshwater strains, a D1:1 isoform of this protein is exchanged for a D1:2 isoform in response to various stresses, thereby altering PSII photochemistry. To investigate PSII responses to stress in marine Synechococcus, we acclimated cultures of the WH7803 strain to different growth irradiances and then exposed them to high light (HL) or ultraviolet (UV) radiation.

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.

Background: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group.

Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study.

Background: Marine Synechococcus owe their specific vivid color (ranging from blue-green to orange) to their large extrinsic antenna complexes called phycobilisomes, comprising a central allophycocyanin core and rods of variable phycobiliprotein composition. Three major pigment types can be defined depending on the major phycobiliprotein found in the rods (phycocyanin, phycoerythrin I or phycoerythrin II). Among strains containing both phycoerythrins I and II, four subtypes can be distinguished based on the ratio of the two chromophores bound to these phycobiliproteins.

High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean Sea in summer.

Natural populations of the marine cyanobacterium Prochlorococcus exist as two main ecotypes, inhabiting different layers of the ocean's photic zone. These so-called high light- (HL-) and low light (LL-) adapted ecotypes are both physiologically and genetically distinct. HL strains can be separated into two major clades (HLI and HLII), whereas LL strains are more diverse.

The cyanobacterial genome core and the origin of photosynthesis.

Comparative analysis of 15 complete cyanobacterial genome sequences, including "near minimal" genomes of five strains of Prochlorococcus spp., revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core CyOGs)] encoded in at least 14 of them. The majority of the core CyOGs are involved in central cellular functions that are shared with other bacteria; 50 core CyOGs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and plants and/or other plastid-carrying eukaryotes, such as diatoms or apicomplexans.

Accelerated evolution associated with genome reduction in a free-living prokaryote.

Background: Three complete genomes of Prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. Comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in G+C content. As all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in Prochlorococcus is the first documented example of such a process in a free-living organism.

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome.

Prochlorococcus marinus, the dominant photosynthetic organism in the ocean, is found in two main ecological forms: high-light-adapted genotypes in the upper part of the water column and low-light-adapted genotypes at the bottom of the illuminated layer. P. marinus SS120, the complete genome sequence reported here, is an extremely low-light-adapted form.