Prokaryotic Cell Abundance Research Articles

Microbial Parameters as Predictors of Heterotrophic Prokaryotic Production in the Ross Sea Epipelagic Waters (Antarctica) during the Austral Summer

A regression-based approach was used to test the suitability of a range of parameters, including total prokaryotic cell abundance and biomass, as lipopolysaccharide (LPS) content, and exoenzymatic activities (leucine aminopeptidase, LAP, beta-glucosidase, ß-G, and alkaline phosphatase, AP) as predictors of heterotrophic prokaryotic production (HPP) in the Ross Sea epipelagic waters. A close association between HPP and protein hydrolysis mediated by enzymatic activity (LAP), and to a lower significance level with the other variables, was recorded. Three multiple regression equations were developed from two microbial datasets collected during middle austral summer periods. All showed a good predictive ability for HPP, and this was further validated through a comparison between the predicted and the observed HPP values. The obtained regression equations proved to represent a promising example of empirical models for further predictive studies in the Ross Sea where—through the incorporation of additional microbiological and environmental parameters—the developed models could find a practical application to cover the entire austral summer period.

Insights into the Methanogenic Population and Potential in Subsurface Marine Sediments Based on Coenzyme F430 as a Function-Specific Biomarker.

Coenzyme F430, the prosthetic group of methyl coenzyme M reductase (MCR), is a key compound in methane metabolism. We applied coenzyme F430 as a function-specific biomarker of methanogenesis to subsurface marine sediments collected below the sulfate reduction zone to investigate the distribution and activity of methanogens. In addition, we examined the kinetics of the epimerization of coenzyme F430, which is the first stage of the degradation process after cell death, at various temperatures (4, 15, 34, 60 °C) and pH (5, 7, 9) conditions, which cover in situ conditions of drilled sediments used in this study. The degradation experiments revealed that the kinetics of the epimerization well follow the thermodynamic laws, and the half-life of coenzyme F430 is decreasing from 304 days to 11 h with increasing the in situ temperature. It indicates that the native F430 detected in the sediments is derived from living methanogens, because the abiotic degradation of F430 is much faster than the sedimentation rate and will not be fossilized. Based on coenzyme F430 analysis and degradation experiments, the native form of F430 detected in subseafloor sediments off the Shimokita Peninsula originates from living methanogen cells, which is protected from degradation in cells but disappears soon after cell death. The biomass of methanogens calculated from in situ F430 concentration and F430 contents in cultivable methanogen species decreases by 2 orders of magnitude up to a sediment depth of 2.5 km, with a maximum value at ∼70 m below the seafloor (mbsf), while the proportion of methanogens to the total prokaryotic cell abundance increases with the depth, which is 1 to 2 orders of magnitude higher than expected previously. Our results indicate the presence of undetectable methanogens using conventional techniques.

The prokaryotic community in an extreme Antarctic environment: the brines of Boulder Clay lakes (Northern Victoria Land)

During summer 2014, three hypersaline brines were discovered in two frozen lakes of Boulder Clay (Northern Victoria Valley, Antarctica). Ongoing research seeks to gain novel insights on the microbial ecology of such environments, in order to further the understanding of life adaptation to extreme conditions. To this aim, the abundance of prokaryotic cells (including cell morphologies and size for biomass conversion), the amount of viable cells (in terms of membrane-intact cells and respiring cells), the viral count, the physiological profiles at community level and the main microbial enzymatic activities were described. The brines differed each other in terms of prokaryotic cells’ abundance, size, and viability as well as viral abundance. Cell morphotypes and metabolic responses also varied among the brine samples. Underground interconnections were likely to occur, with the microbial community becoming more abundant and structured to better exploit the limited resource availability. Overall, complex interactions among multiple environmental factors, including marine water origin, depth horizon, isolation time of the brines, and climatic variations, reflected on the microbial community distribution patterns and highlighted the need to preserve these niches of extreme life.

Recovery of subtropical coastal intertidal system prokaryotes from a destruction event and the role of extracellular polymeric substances in the presence of endocrine disrupting chemicals

Intertidal sediments constitute the micro-environment for the co-existence of endocrine disrupting chemicals (EDCs) and biofilms consisting of the microbial community and extracellular polymeric substances (EPS). However, the interactions and the resulting eco-function of this community are complex and poorly characterized, especially after a destruction event. This study evaluates the re-construction of biofilms in terms of the abundance of prokaryotic cells and related EPS characterization in two destroyed sedimentary matrices from subtropical environments simulated by sterilization in the presence of EDCs and investigates the role of EPS. The results show that benthic prokaryotes recover from the deposition of active prokaryotes in natural seawater and form biofilms after sterilization. Sterilization triggers the release of polysaccharides and protein from lysed native microbial cells and bound EPS in sedimentary organic matter, thus increasing their concentrations. The increased portion of EPS also acts as a persistent stress on re-colonizing prokaryotes and leads to the overproduction of sedimentary EPS. Due to the protective role mediated by EPS, the effect of EDCs on biofilm composition in sterilized sediment is not significant. The sedimentary matrix is the most important determinant of the composition of the biofilm and the occurrence of EDCs. At the end of an 84-day experiment, the abundance of prokaryotic cells and the concentrations of polysaccharides and protein in mangrove sediment are 1.6–1.8 times higher than those in sandflat sediment, regardless of EDCs. Sandflat sediment exhibits higher concentrations of nonylphenol and bisphenol A but a lower concentration of 17α-ethinylestradiol than mangrove sediment. This study enhances our understanding of the role of sedimentary biofilms and the fate of EDCs in intertidal systems and highlights the benefit of a destructive event in enhancing ecosystem function, particularly tolerance to EDC adversity due to EPS production.

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean

BackgroundMarine bacteria form complex relationships with eukaryotic hosts, from obligate symbioses to pathogenic interactions. These interactions can be tightly regulated by bioactive molecules, creating a complex system of chemical interactions through which these species chemically communicate thereby directly altering the host’s physiology and community composition. Quorum sensing (QS) signals were first described in a marine bacterium four decades ago, and since then, we have come to discover that QS mediates processes within the marine carbon cycle, affects the health of coral reef ecosystems, and shapes microbial diversity and bacteria-eukaryotic host relationships. Yet, only recently have alkylquinolone signals been recognized for their role in cell-to-cell communication and the orchestration of virulence in biomedically relevant pathogens. The alkylquinolone, 2-heptyl-4-quinolone (HHQ), was recently found to arrest cell growth without inducing cell mortality in selected phytoplankton species at nanomolar concentrations, suggesting QS molecules like HHQ can influence algal physiology, playing pivotal roles in structuring larger ecological frameworks.ResultsTo understand how natural communities of phytoplankton and bacteria respond to HHQ, field-based incubation experiments with ecologically relevant concentrations of HHQ were conducted over the course of a stimulated phytoplankton bloom. Bulk flow cytometry measurements indicated that, in general, exposure to HHQ caused nanoplankton and prokaryotic cell abundances to decrease. Amplicon sequencing revealed HHQ exposure altered the composition of particle-associated and free-living microbiota, favoring the relative expansion of both gamma- and alpha-proteobacteria, and a concurrent decrease in Bacteroidetes. Specifically, Pseudoalteromonas spp., known to produce HHQ, increased in relative abundance following HHQ exposure. A search of representative bacterial genomes from genera that increased in relative abundance when exposed to HHQ revealed that they all have the genetic potential to bind HHQ.ConclusionsThis work demonstrates HHQ has the capacity to influence microbial community organization, suggesting alkylquinolones have functions beyond bacterial communication and are pivotal in driving microbial community structure and phytoplankton growth. Knowledge of how bacterial signals alter marine communities will serve to deepen our understanding of the impact these chemical interactions have on a global scale.

Decoding the ocean's microbiological secrets for marine enzyme biodiscovery.

A global census of marine microbial life has been underway over the past several decades. During this period, there have been scientific breakthroughs in estimating microbial diversity and understanding microbial functioning and ecology. It is estimated that the ocean, covering 71% of the earth's surface with its estimated volume of about 2 × 1018 m3 and an average depth of 3800 m, hosts the largest population of microbes on Earth. More than 2 million eukaryotic and prokaryotic species are thought to thrive both in the ocean and on its surface. Prokaryotic cell abundances can reach densities of up to 1012 cells per millilitre, exceeding eukaryotic densities of around 106 cells per millilitre of seawater. Besides their large numbers and abundance, marine microbial assemblages and their organic catalysts (enzymes) have a largely underestimated value for their use in the development of industrial products and processes. In this perspective article, we identified critical gaps in knowledge and technology to fast-track this development. We provided a general overview of the presumptive microbial assemblages in oceans, and an estimation of what is known and the enzymes that have been currently retrieved. We also discussed recent advances made in this area by the collaborative European Horizon 2020 project ‘INMARE’.

Virus morphological diversity and relationship to bacteria and chlorophyll across a freshwater trophic gradient in the Lake Michigan watershed

The critical roles of viruses in nutrient cycling are well established for marine ecosystems, but less is known for freshwater viruses about diversity, seasonality, and relationships with productivity and ecosystem trophic status. This study aimed to examine virus morphotypes and abundance in relation to prokaryotic cell abundance and chlorophyll a concentrations in three seasonal temperate freshwater sites representing eutrophic, mesotrophic, and oligotrophic status in Lake Michigan watershed. We found strong correlations between virus-like particle abundance (VLPA) and prokaryote abundance (PA) and chlorophyll concentration across the trophic gradient (r = 0.744, P < 0.001, n = 123), but without consistent seasonal patterns. TEM showed Myoviridae, Podoviridae, Siphoviridae, and non-tailed virus morphotypes. The eutrophic site was distinct with one- to two-fold higher PA and VLPA than mesotrophic and oligotrophic sites. But the eutrophic and mesotrophic sites had more similar VLPA:PA ratios (eutrophic 26, mesotrophic 25.5, oligotrophic 4.1). The oligotrophic site also had a lower proportion of Podoviridae and more Siphoviridae than the other sites. The similarity between eutrophic and mesotrophic sites, but a distinctive oligotrophic site, suggests that the effects of terrestrial runoff as sources of viruses and hosts may be important, along with P limitation and trophic status, in determining virus–host relationships in freshwaters.

Co-occurrence of integrase 1, antibiotic and heavy metal resistance genes in municipal wastewater treatment plants

The impact of human activities on the spread and on the persistence of antibiotic resistances in the environment is still far from being understood. The natural background of resistances is influenced by human activities, and the wastewater treatment plants (WWTPs) are among the main sources of the release of antibiotic resistance into the environment. The various treatments of WWTPs provide a number of different environmental conditions potentially favoring the selection of antibiotic resistance genes (ARGs) and thereby their well-documented spread in the environment. Although the distribution of different ARGs in WWTPs has been deeply investigated, very little is known on the ecology and on the molecular mechanisms underlying the selection of specific ARGs. This study investigates the fate of diverse ARGs, heavy metal resistance genes (HMRGs) and of a mobile element (the class I integron) in three WWTPs. Abundances of the different genetic markers were correlated to each other and their relation to biotic and abiotic factors (total organic carbon, total nitrogen, prokaryotic cell abundance and its relative distribution in single cells and aggregates) influencing the microbial communities in the different treatment phases in three WWTPs, were investigated. Water samples were analyzed for the abundance of six ARGs (tetA, sulII, blaTEM, blaCTXM,ermB, and qnrS), two HMRGs (czcA and arsB), and of the class I integron (int1). The measured variables clustered in two well-defined groups, the first including tetA, ermB, qnrS and the different biotic and abiotic factors, and a second group around the genes sulII, czcA, arsB and int1. Moreover, the dynamics of sulII, HMRGs, and int1 correlated strongly. Our results suggest a potentially crucial role of HMRGs in the spread, mediated by mobile elements, of some ARGs, i.e. sulII. The possibility of a relation between heavy metal contamination and the spread of ARGs in WWTPs calls for further research to clarify the mechanisms of co-selection and their ecology, in order to implement the removal efficiency of the applied treatments.

Bacterial and macrofaunal communities in the sediments of the West Gironde Mud Patch, Bay of Biscay (France)

Changes in (1) main sediment characteristics, and (2) benthic bacterial and macrofaunal communities were simultaneously addressed along an inner–outer transect within the West Gironde Mud Patch (Bay of Biscay, NE Atlantic), through the sampling of three stations (E: inner part, C: central part and W: outer part) during July 2010. Except in the top centimetre where a sandy layer was found at station E, all sediments were muddy and tended to be coarser and richer in photosynthetic pigments and particulate organic carbon and nitrogen at stations C and W than at station E. Maximum oxygen penetration depth was also lower at station E than at stations C and W. These results are consistent with: (1) the occurrence of strong hydrodynamics precluding current sedimentation in the inner part of the WGMP, and (2) conversely, inputs of particles originating from the Gironde Estuary in its central and outer part. Prokaryotic cell abundances were lower at station E than at stations C and W. Bacterial community composition also differed more clearly at station E as compared to stations C and W. Conversely, macrofaunal abundances and species richness decreased monotonously from station E to station W (i.e., along the inner–outer gradient). Macrofaunal composition strongly differed at station E on one side, and stations C and W on the other side. These results are consistent with the current paradigm regarding the long term effect of major rivers on benthic macrofauna given that strong hydrodynamics at station E precludes the sedimentation of fine particles originating from the Gironde Estuary. At last, we found no overall correlation between benthic bacterial and macrofaunal compositions, which may however clearly result from limitations in our sampling design.

Quantification of aquatic sediment prokaryotes—A multiple-steps optimization testing sands from pristine and contaminated aquifers

The total number of prokaryotic cells in aquatic sediments is a crucial measure tightly linked to energetic constraints, microbial productivity, and ecosystem status. While counting cells in water samples is routine, reliable procedures for the determination of prokaryotic cells associated to aquatic sediments are especially needed. A protocol for the direct quantification of prokaryotic cell abundance in aquatic sediments was developed and tested with sandy material from pristine and contaminated aquifers. Individual steps required in sample preparation, including preservation, cell dislodgement, density gradient centrifugation providing sample purification, and staining, were critically evaluated and optimized. Quantification of cells is conducted by flow cytometry promoting a high-throughput sample processing. Although tested for only two different types of aquifer sediments, researchers may easily adapt the protocol for their individual samples and purposes, thus conducting a brief efficiency re-evaluation of individual steps highlighted in this study.

Bacterial and Archaeal Communities Variability Associated with Upwelling and Anthropogenic Pressures in the Protection Area of Arraial do Cabo (Cabo Frio region - RJ).

Upwelling systems contain a high diversity of pelagic microorganisms and their composition and activity are defined by factors like temperature and nutrient concentration. Denaturing gradient gel electrophoresis (DGGE) technique was used to verify the spatial and temporal genetic variability of Bacteria and Archaea in two stations of the Arraial do Cabo coastal region, one under upwelling pressure and another under anthropogenic pressure. In addition, biotic and abiotic variables were measured in surface and deep waters from three other stations between these stations. Six samplings were done during a year and adequately represented the degrees of upwelling and anthropogenic pressures to the system. Principal Component Analysis (PCA) showed negative correlations between the concentrations of ammonia and phosphorous with prokaryotic secondary production and the total heterotrophic bacteria. PCA also showed negative correlation between temperature and the abundance of prokaryotic cells. Bacterial and archaeal compositions were changeable as were the oceanographic conditions, and upwelling had a regional pressure while anthropogenic pressure was punctual. We suggest that the measurement of prokaryotic secondary production was associated with both Bacteria and Archaea activities, and that substrate availability and temperature determine nutrients cycling.

Effects of mass sedimentation events after the 2011 off the Pacific coast of Tohoku Earthquake on benthic prokaryotes and meiofauna inhabiting the upper bathyal sediments

We examined the effects of mass sedimentation events caused by the 2011 off the Pacific coast of Tohoku Earthquake on abundances and vertical distributions of prokaryotes and metazoan meiofauna in sediments, using sediment cores collected from eight bathyal stations off Tohoku 1 year after the M9.0 earthquake. Event deposits 1–7 cm thick were observed at the topmost part of the sediment cores at all sampling stations. At some stations, prokaryotic cell abundances were lower in the surface event-deposit layers compared to those in deeper sediments. These variations were explained by environmental parameters such as a dimensionless sorting factor and mean grain size, suggesting that turbidite sedimentation affected prokaryotic cell abundances. Nematodes had anomalously higher subsurface abundances at the stations where subsurface peak prokaryotic cell numbers were observed, whereas copepods always showed peak densities in the sediment surface layer. Although there are no available data for prokaryotic cell abundances and meiofaunal densities before the earthquake from the same sites, it is likely that the subsurface peaks in prokaryotic cell numbers and nematode densities resulted from the sedimentation events. The effects of sedimentation events on the organisms were observed 1 year after the earthquake, indicating that episodic sedimentation events on scales of several centimeters have a large effect on small organisms inhabiting sediments.

Are prokaryotic cell shape and size suitable to ecosystem characterization?

Estimation of microbial biomass depends on cell shape and size determinations, and thus, there is a wide biovolume variability among morphotypes. Nevertheless, data on morphology and morphometry of prokaryotic cells under different trophic status are seldom published, due to the methodological difficulties of cell measurements. The main question addressed in this paper concerns the suitability of prokaryotic size and shape for environmental characterization. Microbial biovolumes were compared among different ecosystems, located in temperate and tropical regions. Samples were taken from fresh, brackish, mixohaline, and estuarine waters that were classified as oligo-, meso-, eu-, and hypertrophic by comparing synoptically different trophic indices. Prokaryotic cell abundance and volume were quantified by Image Analysis, used to calculate biomass, and correlated to environmental variables. Some samples were analyzed by flow cytometry also, and data from sub-populations with a different apparent DNA content were available. Prokaryotic abundances generally increased from oligo- to hypertrophic waters while cell volumes increased from oligotrophic to eutrophic waters. Although significant correlations between cell volumes and environmental variables were detected (positive with salinity and negative with Chlorophyll-a), different morphotypes dominated each studied regions. Our results sustain the hypothesis that prokaryotic cell size and shape could be useful to ecosystem characterization.

Microbial abundance in the coelenteron and mucus of the cold-water coral Lophelia pertusa and in bottom water of the reef environment

AB Aquatic Biology Contact the journal Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections AB 16:209-216 (2012) - DOI: https://doi.org/10.3354/ab00443 Microbial abundance in the coelenteron and mucus of the cold-water coral Lophelia pertusa and in bottom water of the reef environment Markus G. Weinbauer1,2,*, Julie Ogier3, Cornelia Maier1,2,3 1INSU-CNRS, Laboratoire d’Océanographie de Villefranche, UMR 7093, BP 28, 06234 Villefranche-sur-Mer Cedex, France 2Université Pierre et Marie-Curie-Paris, Laboratoire d’Océanographie de Villefranche, UMR 7093, 06230 Villefranche-sur-mer, France 3Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO Box 59, 1790 AB Den Burg, Texel, The Netherlands *Email: wein@obs-vlfr.fr ABSTRACT: Microorganisms play an important role in coral ecology; however, little is known about cold-water coral (CWC) reefs. Microbial abundance in bottom water of Lophelia pertusa-dominated CWC reefs in the Skagerrak, North Sea, was elevated by ca. 40% for prokaryotes and 70 to 90% for viruses compared to bottom water where no corals were present. This indicates that CWCs influence the microbial food web in bottom water. Furthermore, results suggest that microorganisms contributed significantly to the stock of organic nitrogen (13%) and organic phosphorus (32%) in bottom water. Prokaryotic abundances in the coelenteron of freshly collected corals were (2.0 ± 0.2) × 107 cells ml−l and viral abundances were (4.0 ± 0.6) × 107 particles ml−l. Prokaryotic abundances in coral mucus were (7.5 ± 0.7) × 107 cells ml−l and viral abundances were (1.7 ± 0.3) × 108 particles ml−l. Onboard incubations with elevated prokaryotic and viral abundances in the incubation water indicated that (1) corals accumulate microorganisms in the coelenteron as a potential food source and (2) control mechanisms exist for the abundance of prokaryotic cells and viral particles in the mucus. Our data suggest that L. pertusa controls microbial biomass in the CWC reef environment and coral microhabitats. KEY WORDS: Cold-water coral · Microbial abundance · Lophelia pertusa · Viruses · Prokaryotes · Bacteria · Reefs Full text in pdf format PreviousNextCite this article as: Weinbauer MG, Ogier J, Maier C (2012) Microbial abundance in the coelenteron and mucus of the cold-water coral Lophelia pertusa and in bottom water of the reef environment. Aquat Biol 16:209-216. https://doi.org/10.3354/ab00443 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AB Vol. 16, No. 3. Online publication date: September 05, 2012 Print ISSN: 1864-7782; Online ISSN: 1864-7790 Copyright © 2012 Inter-Research.

Viruses in a deep oligotrophic sea: Seasonal distribution of marine viruses in the epi-, meso- and bathypelagic waters of the Eastern Mediterranean Sea

Marine viruses and their main hosts were studied in the Eastern Mediterranean Sea (Ionian, Libyan and Aegean Seas) during two sampling cruises (mixing and water column stratification periods). Samples were collected from the surface to 4000m depth. Total abundance of viruses and prokaryotes was determined by Flow Cytometry (FCM). Viruses were separated into three groups according to their fluorescence signal. Viral abundance ranged from 1.2×105viruses ml−1 to 2.7×107virusesml−1 and varied significantly between areas, depth zones and seasons. Prokaryotic cell abundance varied from 1.7×104cellsml−1 to 1.5×106cellsml−1 presenting a strong positive correlation with viral abundance. Stations and depths influenced by the Black Sea Water in the North Aegean Sea presented the highest values of viral abundance and Viruses to Prokaryotes Ratio (VPR). Vertical distributions of VPR were attributed to different water masses. The increased viral abundance and VPR values that were detected during the stratification period may be explained by the seasonal changes in prokaryotic cell characteristics (cell size, nucleic acid content). These significant seasonal distributions were also found below 1000m indicating a possible viral activity in the bathypelagic ocean.

Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

Domain‐level identification and quantification of relative prokaryotic cell abundance in microbial communities by Micro‐FTIR spectroscopy

Domain-level identification of microbial cells or cell-like structures is crucial for investigating natural microbial communities and their ecological significance. By using micro-Fourier transform infrared (micro-FTIR) spectroscopy, we established a technical basis for the domain-level diagnosis and quantification of prokaryotic cell abundance in natural microbial communities. Various prokaryotic cultures (12 species of bacteria and 10 of archaea) were examined using micro-FTIR spectroscopic analysis. The aliphatic CH3 /CH2 absorbance ratios (R3/2 ) showed domain-specific signatures, possibly reflecting distinctive cellular lipid compositions. The signatures were preserved even after chemical cell fixation (formaldehyde) and nucleic acid staining (DAPI) processes - techniques that are essential in studying microbial ecology. The micro-FTIR technique was successfully applied for quantification of the bacteria/archaea abundance ratio in an active microbial mat community in a subsurface hot aquifer stream. We conclude that the micro-FTIR R3/2 measurement is both fast and effective for domain-level diagnosis and quantification of first-order prokaryotic community structures.

Response of soil microbial communities to the herbicide mesotrione: A dose-effect microcosm approach

Mesotrione is a new selective herbicide used for maize crops. The responses of microbial communities of a chernozem soil (Limagne basin, France) to pure or formulated (Callisto ®) mesotrione, applied at three different doses [one fold field rate (1 × FR), 10 × FR and 100 × FR], were studied using a laboratory microcosm approach. The effects were assessed on the prokaryotic cell abundance, the overall microbial activities (substrate-induced respiration (SIR) and dehydrogenase activity (DHA)) and the genetic structure of the bacterial and fungal communities (temporal temperature/denaturing gradient gel electrophoresis (TT/DGGE)). Mesotrione dissipation was similar whatever the formulation applied and the amounts dissipated were positively correlated to application rates. Several biodegradation products including the metabolites 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4-methylsulfonylbenzoic acid (AMBA) were detected from day 42 post-treatment, in 10 × FR and 100 × FR treated soils. No response of the soil microbial communities was detected in soil spread with both the 1 × FR applications. Overall soil microbial activity was stimulated from day 6 by 10 × FR of Callisto ® and more strongly by 100 × FR of pure mesotrione and Callisto ®, whereas prokaryote abundance did not increase before day 95 in both the 100 × FR treatments. Genetic structural shifts recorded from day 42 in the bacterial and fungal communities were small and mainly attributable to variations in band intensity. Maximum dissimilarity of the bacterial and fungal genetic structures between control and 100 × FR treated soils did not exceed 12% and 28%, respectively. The general pattern was that more consistent effects occurred with increasing exposure times, especially in both the 100 × FR treated soils. These microbial responses could be due to the stimulation of (i) adapted mesotrione-degrading microorganisms and (ii) the activity of resistant heterotrophic microbial groups promoted by dead biomass from sensitive organisms. In addition, at 100 × FR doses, pure mesotrione seemed to induce stronger microbial responses than Callisto ®, formulation which contains adjuvants with potential side-effects on some microbial populations. This experimental approach indicated that pure mesotrione and Callisto ® affected soil microbial communities, but the effects were only detected at doses far exceeding the recommended field rates.

Apparent richness and community composition of Bacteria and Archaea in geothermal springs

The archaeal and bacterial 16S rRNA gene diversities of the Polihnitos (89°C), Edipsos (81.8°C), Thermopiles (38.9°C), Eleftheres (41.2°C) and Lagadas (35.2°C) geothermal springs in Greece were investigated. The abundance of prokaryotic cells varied between 0.02 × 10 5 and 0.92 × 10 5 cells ml -1 . A total of 227 archaeal and 501 bacterial clones were analysed, which were attributed to 85 and 121 operational taxonomic units (OTUs), respectively. Library clone coverage, based on Good's C estimator, was satisfactory (>75%), except for the Archaea in Thermopiles (~40%) and Eleftheres (~60%). Most of the archaeal phylotypes were related to sequences of yet-uncultivated microorganisms retrieved from terrestrial geothermal springs, deep-sea hydrothermal vents and the subsurface. A much higher number of bacterial phylotypes was related to cultivated microorganisms from similar environments. The thermophilic nature of most of the discovered phylotypes was also supported by their high G+C content, which was positively correlated with the springs' temperatures. The springs showed different diversity patterns for Bacteria and Archaea, with Bacteria having higher diversity only in Polihnitos and Lagadas springs. The Shannon diversity index H' showed larger variation for Archaea (0.23 to 3.44) than for Bacteria (1.22 to 3.03) and was unrelated to the pre- vailing temperature, pH, salinity and dissolved oxygen content. Archaeal and bacterial clone libraries respectively contained 50 to 94.1 and 68.8 to 96.2% rare phylotypes (i.e. those that appear only once or twice in the clone library), indicating the importance of rare phylotypes in shaping com- munity diversity.

Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin

The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average approximately 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.