Prokaryotic Abundance Research Articles

Full-depth profiles of prokaryotes, heterotrophic nanoflagellates, and ciliates along a transect from the equatorial to the subarctic central Pacific Ocean

Studies in epipelagic waters report higher heterotrophic microbial biomass in the productive high latitudes than in the oligotrophic low latitudes; however, biogeographical data are scarce in the deep ocean. To examine the hypothesis that the observed latitudinal differences in heterotrophic microbial biomass in the epipelagic zone also occur at depth, abundance and biomass of heterotrophic prokaryotes, nanoflagellates (HNF), and ciliates were determined at depths of 5-5000 m in the central Pacific between August and September of 2005. Heterotrophic microbial biomass increased from the tropical to the subarctic region over the full water column, with latitudinal differences in prokaryotic biomass increasing from 2.3-fold in the epipelagic zone to 4.4-fold in the bathypelagic zone. However, the latitudinal difference in HNF and ciliate biomass decreased with depth. In the mesopelagic zone, the vertical attenuation rate of prokaryotic abundance, which was calculated as the linear regression slope of log-log plot of abundance versus depth, ranged from -0.55 to -1.26 and was more pronounced (steeper slope) in the lower latitudes. In contrast, the vertical attenuation rate of HNF in the mesopelagic zone (-1.06 to -1.27) did not differ with latitude. In the subarctic, the attenuation rate of HNF was 1.7 times steeper than for prokaryotes. These results suggest the accumulation of prokaryotes in the deep subarctic Pacific, possibly due to low grazing pressure. Although the vertical attenuation rate of ciliates was steepest in the bathypelagic zone, HNF abundance did not further decrease at depths below 1000 m, except for at 2000 m where HNF was lowest across the study area. Ciliate abundance ranged 0.3-0.8 cells l -1 at 4000 m, and were below the detection limit ( < 0.1 cells l -1 ) at 5000 m. To our knowledge, this study presents the first data for ciliates below 2000 m.

Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics

This paper synthesizes recent findings regarding microbial distributions and processes in the bathypelagic ocean (depth >1000 m). Abundance, production and respiration of prokaryotes reflect supplies of particulate and dissolved organic matter to the bathypelagic zone. Better resolution of carbon fluxes mediated by deep microbes requires further testing on the validity of conversion factors. Archaea, especially marine Crenarchaeota Group I, are abundant in deep waters where they can fix dissolved inorganic carbon. Viruses appear to be important in the microbial loop in deep waters, displaying remarkably high virus to prokaryote abundance ratios in some oceanic regions. Sequencing of 18S rRNA genes revealed a tremendous diversity of small-sized protists in bathypelagic waters. Abundances of heterotrophic nanoflagellates (HNF) and ciliates decrease with depth more steeply than prokaryotes; nonetheless, data indicated that HNF consumed half of prokaryote production in the bathypelagic zone. Aggregates are important habitats for deep-water microbes, which produce more extracellular enzymes (on a per-cell basis) than surface communities. The theory of marine gel formation provides a framework to unravel complex interactions between microbes and organic polymers. Recent data on the effects of hydrostatic pressure on microbial activities indicate that bathypelagic microbial activity is generally higher under in situ pressure conditions than at atmospheric pressures. High-throughput sequencing of 16S rRNA genes revealed a remarkable diversity of Bacteria in the bathypelagic ocean. Metagenomics and comparative genomics of piezophiles reveal not only the high diversity of deep sea microbes but also specific functional attributes of these piezophilic microbes, interpreted as an adaptation to the deep water environment. Taken together, the data compiled on bathypelagic microbes indicate that, despite high-pressure and low-temperature conditions, microbes in the bathypelagic ocean dynamically interact with complex mixtures of organic matter, responding to changes in the ocean’s biogeochemical state.

Impact of Arenicola marina (Polychaeta) on the microbial assemblages and meiobenthos in a marine intertidal flat

The benthic microbial food web can be responsible for a large proportion of benthic carbon cycling yet there are few data on the trophic interactions between this food web and macrobenthos. A large-scale field experiment was conducted to investigate effects of eliminating the polychaete Arenicola marina on benthic microbes (prokaryotes, heterotrophic and autotrophic protists) and metazoan meiofauna in a marine intertidal flat of the North Sea, Germany. Over a period of 2 years, quantity and composition of micro- and meiobenthos from unmanipulated sites were compared to those from sites deplete of lugworms. These grazer treatments were cross-classified with different sediment characteristics (low- and mid-intertidal areas). Lugworm removal resulted in an initial increase in abundance of prokaryotes and nanoflagellates, which became less pronounced in the second year. Ciliates were not affected quantitatively, but in the absence of lugworms, diversity and the proportion of carnivorous forms increased. Meiobenthos (nematodes, ostracods and copepods) were affected only moderately. The observed changes are probably due to a combination of release from grazing/predation pressure, changes in the species composition of higher trophic levels (namely large polychaetes) and altered environmental conditions (such as depth of the oxygenated layer and sediment grain size). Spatial differences between sites of different tidal exposure/grain size appeared to be as large as temporal differences during the 2 years following the manipulation of the system. We conclude that in intertidal sediments, indirect effects due to habitat transformation are as important as direct biological interactions (grazing pressure and competition) for the dynamics of the benthic microbial food web.

High dissolved extracellular enzymatic activity in the deep central Atlantic Ocean

The distribution of prokaryotic abundance (PA), prokaryotic heterotrophic production (PHP), and suspended particulate organic material (POM), as well as total and dissolved (operationally defined as passing through 0.2 mu m pore size filters) potential extracellular enzymatic activities (EEA; alpha- and beta-glucosidase [AGase and BGase], leucine aminopeptidase [LAPase], and alkaline phosphatase [APase]) were determined in the meso- and bathypelagic waters of the (sub)tropical Atlantic along an eastern zonal transatlantic transect and a western N-S transect. Significant differences between both transects were found for POM concentration but not for PA, PHP (except in the subsurface and oxygen minimum layer), and dissolved and total EEA. PHP decreased by 3 orders of magnitude from the lower euphotic zone to bathypelagic waters, while PA and cell-specific PHP decreased only by 1 and 2 orders of magnitude, respectively. The proportion of the dissolved to the total EEA was high in the dark ocean for all the enzymes, ranging from 54 to 100, 56 to 100, 65 to 100 and 57 to 97 % for AGase, BGase, LAPase and APase, respectively. The kinetic parameters (V-max, and K-m) of both the dissolved and total fractions of LAPase and APase were very similar throughout the water column, suggesting a similar origin for both dissolved and particulate EEA. Significant correlations of both dissolved and total EEA were found with prokaryotic metabolism and the POM pool. Based on the previous notion that the fraction of dissolved EEA is higher in particle-attached than in free-living microbes, our results suggest that microbial activity in the dark ocean occurs mainly on colloidal and particulate material. This is in agreement with recent genomic evidence. However, these colloidal and particulate materials are prone to disruption during the sampling process. Hence, more selective sampling techniques are needed to specifically collect these deep-water aggregates that probably represent hotspots of microbial activity in the deep ocean.

Luminous bacteria in the deep-sea waters near the ANTARES underwater neutrino telescope (Mediterranean Sea)

Marine luminous deep-sea bacteria may represent a potential source of signal perturbation for the ANTARES neutrino telescope installed between 2000 and 2475 m depth in the Mediterranean Sea. Using the CARD-FISH method, we have estimated the relative abundances of total prokaryotes of Bacteria, γ -proteobacteria and Vibrinoceae (domain, class and family affiliation of marine luminous bacteria, respectively) through the water column close to the ANTARES site. At 2200 m depth, Vibrionaceae appeared to be far from negligible, representing 40% of γ -proteobacteria, 25% of Bacteria and 9% of the total DAPI-stained cells, while Bacteria and Archaea represented 35% each. Furthermore, during a high luminous background period detected by the neutrino telescope, we isolated, from a 2200 m depth sample, a piezophilic luminous bacterium, phylogenetically determined as Photobacterium phosphoreum strain ANT-2200. We have used this strain to investigate the effect of hydrostatic pressure on bioluminescence by developing a new high-pressure apparatus. First assays showed that the bioluminescence intensity of Photobacterium phosphoreum strain ANT-2200 was 5 times higher at 22 MPa than at 0.1 MPa (atmospheric pressure).

Prokaryotic aminopeptidase activity along a continuous salinity gradient in a hypersaline coastal lagoon (the Coorong, South Australia)

The distribution and aminopeptidase activity of prokaryotes were investigated along a natural continuous salinity gradient in a hypersaline coastal lagoon, the Coorong, South Australia. The abundance of prokaryotes significantly increased from brackish to hypersaline waters and different sub-populations, defined by flow cytometry, were observed along the salinity gradient. While four sub-populations were found at each station, three additional ones were observed for 8.3% and 13.4%, suggesting a potential modification in the composition of the prokaryotic communities and/or a variation of their activity level along the salinity gradient. The aminopeptidase activity highly increased along the gradient and salinity appeared as the main factor favouring this enzymatic activity. However, while the aminopeptidase activity was dominated by free enzymes for salinities ranging from 2.6% to 13.4%, cell-attached aminopeptidase activity was predominant in more saline waters (i.e. 15.4%). Changes in substrate structure and availability, strongly related to salinity, might (i) modify patterns of both aminopeptidase activities (free and cell-associated enzymes) and (ii) obligate the prokaryotic communities to modulate rapidly their aminopeptidase activity according to the nutritive conditions available along the gradient.

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.

Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment

Sulfate-reducing prokaryotes (SRP) cause severe problems like microbial corrosion and reservoir souring in seawater-injected oil production systems. One strategy to control SRP activity is the addition of nitrate to the injection water. Production waters from two adjacent, hot (80 degrees C) oil reservoirs, one with and one without nitrate treatment, were compared for prokaryotic community structure and activity of SRP. Bacterial and archaeal 16S rRNA gene analyses revealed higher prokaryotic abundance but lower diversity for the nitrate-treated field. The 16S rRNA gene clone libraries from both fields were dominated by sequences affiliated with Firmicutes (Bacteria) and Thermococcales (Archaea). Potential heterotrophic nitrate reducers (Deferribacterales) were exclusively found at the nitrate-treated field, possibly stimulated by nitrate addition. Quantitative PCR of dsrAB genes revealed that archaeal SRP (Archaeoglobus) dominated the SRP communities, but with lower relative abundance at the nitrate-treated site. Bacterial SRP were found in only low abundance at both sites and were nearly exclusively affiliated with thermophilic genera (Desulfacinum and Desulfotomaculum). Despite the high abundance of archaeal SRP, no archaeal SRP activity was detected in [(35)S]sulfate incubations at 80 degrees C. Sulfate reduction was found at 60 degrees C in samples from the untreated field and accompanied by the growth of thermophilic bacterial SRP in batch cultures. Samples from the nitrate-treated field generally lacked SRP activity. These results indicate that (i) Archaeoglobus can be a major player in hot oil reservoirs, and (ii) nitrate may act in souring control-not only by inhibiting SRP, but also by changing the overall community structure, including the stimulation of competitive nitrate reducers.

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.

Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso‐ and bathypelagic waters of the (sub)tropical Atlantic

Prokaryotic extracellular enzymatic activity, abundance, heterotrophic production and respiration were determined in the meso- and bathypelagic (sub)tropical North Atlantic. While prokaryotic heterotrophic production (PHP) decreased from the lower euphotic layer to the bathypelagic waters by two orders of magnitude, prokaryotic abundance and cell-specific PHP decreased only by one order of magnitude. In contrast to cell-specific PHP, cell-specific extracellular enzymatic activity (alpha- and beta-glucosidase, leucine aminopeptidase, alkaline phosphatase) increased with depth as did cell-specific respiration rates. Cell-specific alkaline phosphatase activity increased from the intermediate water masses to the deep waters up to fivefold. Phosphate concentrations, however, varied only by a factor of two between the different water masses, indicating that phosphatase activity is not related to phosphate availability in the deep waters. Generally, cell-specific extracellular enzymatic activities were inversely related to cell-specific prokaryotic leucine incorporation. Thus, it is apparent that the utilization of deep ocean organic matter is linked to higher cell-specific extracellular enzymatic activity and respiration and lower cell-specific PHP than in surface waters.

Seasonal and depth-related dynamics of prokaryotes and viruses in surface and deep waters of the northwestern Mediterranean Sea

The study site located in the northwestern Mediterranean Sea was visited nine times in 2005–2006 to collect water samples from the epi- (5 m), meso- (200, 600 m), and bathypelagic (1000, 2000 m) zone. Total abundance of prokaryotes and viruses was determined by flow cytometry (FCM). Prokaryotic abundance in the epi-, meso-, and bathypelagic varied between 0.9 and 15.9×10 5, 0.6 and 2.1×10 5, and 0.3 and 1.3×10 5 ml −1, respectively. Variation of viral abundance in the epi-, meso-, and bathypelagic was between 1.2 and 57.5×10 6, 0.5 and 3.5×10 6, and 0.4 and 1.3×10 6 ml −1, respectively. The fraction of low (LNA) and high (HNA) nucleic acid prokaryotes averaged 42.9% and 57.1% throughout the water column and did not differ between depth layers. Throughout the water column the fraction of low, medium, and high fluorescent viruses (Vir-LF, Vir-MF, Vir-HF) averaged 66.3%, 30.2%, and 3.5%. Vir-LF and Vir-MF did not differ between depth layers; however, Vir-HF showed a preference for surface waters. The fraction of LNA cells decreased in the epi- and increased in the bathypelagic with decreasing stratification. The fraction of Vir-LF viruses increased in the epipelagic and decreased in the bathypelagic with increasing prokaryotic abundance. Also, the relationship between viral abundance and the bacterial community was different in surface and deep waters. The data suggest that different mechanisms of interaction between viruses and their prokaryotic hosts prevail at the surface and in deep waters.

Role of mesoscale cyclonic eddies in the distribution and activity of Archaea and Bacteria in the South China Sea

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 56:65-79 (2009) - DOI: https://doi.org/10.3354/ame01324 Role of mesoscale cyclonic eddies in the distribution and activity of Archaea and Bacteria in the South China Sea Yao Zhang1, Eva Sintes2, Jianing Chen1, Yong Zhang1, Minhan Dai1, Nianzhi Jiao1, Gerhard J. Herndl2,3,* 1State Key Laboratory for Marine Environmental Sciences, Xiamen University, 422 Siming South Road, Xiamen 361005, China 2Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO Box 59, 1790 AB Den Burg, The Netherlands 3University of Vienna, Ecology Center, Department of Marine Biology, Althanstr. 14, 1090 Vienna, Austria *Corresponding author. Email: gerhard.herndl@univie.ac.at ABSTRACT: We examined the effect of 2 cold-core cyclonic eddies on the activity of the prokaryotic plankton community in the South China Sea. The abundance of bulk prokaryotes and major prokaryotic groups (Bacteria, marine Crenarchaeota Group I and marine Euryarchaeota Group II) and the number of cells taking up D- vs. L-aspartic acid (Asp) were determined using microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization (MICRO-CARD-FISH). At all sites, the bulk D-Asp:L-Asp uptake ratio by the prokaryotic community increased with depth. Concurrently, the contribution of marine Crenarchaeota Group I to total prokaryotic abundance and total active cells also increased with depth, while an opposite pattern was observed for Bacteria. Marine Euryarchaeota Group II were generally more dominant in near-surface than in deep waters. Significant differences were observed between sites inside and outside the cyclonic eddies in terms of distribution and activity of prokaryotic communities and the concentration of fluorescent dissolved organic matter (FDOM, an important refractory fraction of DOM). Generally, higher bulk D-Asp:L-Asp uptake ratios by the prokaryotic community and a greater crenarchaeotal contribution were found in the upper mesopelagic water column inside the cold-core eddies as compared to the outside sites. Taken together, the MICRO-CARD-FISH data and the pattern of FDOM indicate that the higher contribution of refractory DOM induced by upwelled water in the cyclonic eddy may have led to a more prominent role of Crenarchaeota in the organic carbon cycling in the mesopelagic realm of the cold-core eddy than outside the eddy in the South China Sea. KEY WORDS: Cyclonic eddy · Archaea · Bacteria · Enantiomeric amino acid uptake · DOM fluorescence Full text in pdf format PreviousNextCite this article as: Zhang Y, Sintes E, Chen J, Zhang Y, Dai M, Jiao N, Herndl GJ (2009) Role of mesoscale cyclonic eddies in the distribution and activity of Archaea and Bacteria in the South China Sea. Aquat Microb Ecol 56:65-79. https://doi.org/10.3354/ame01324 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 56, No. 1. Online publication date: July 09, 2009 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2009 Inter-Research.

Seasonal Depth-Related Gradients in Virioplankton: Standing Stock and Relationships with Microbial Communities in Lake Pavin (France)

This study presents a depth-related survey of virioplankton abundance in Lake Pavin (Massif Central, France), in relation to the abundances of heterotrophic prokaryotes, picocyanobacteria (Pcy), autotrophic picoeukaryotes (Peu), and of autotrophic (ANF) and heterotrophic (HNF) nanoflagellates. The sampling strategy was designed to be representative of the physico-chemical gradients of the whole water column of the lake, and the seasonal variability as well. In mixolimnic surface waters, all communities were present and viral abundance peaked in summer and autumn. Viral abundance was significantly correlated (p < 0.001) with Pcy, Peu, and ANF, indicating that cyanophages and perhaps other phytoplankton viruses represent a significant pool of viral standing stocks in the mixolimnion of Lake Pavin. Microautotrophs were absent in the deep monimolimnic water masses, where viruses and heterotrophic prokaryotes exhibited highest seasonal abundances in summer and/or autumn and were significantly correlated (p < 0.001) to each other. This indicates that the anoxic monimolimnion of Lake Pavin is an exclusive habitat for viruses and heterotrophic prokaryotes. We conclude that in this habitat, host availability is prevalent over other factors (temperature, oxygen, nutrients, grazers) in favoring viral proliferation.

Viral and Flagellate Control of Prokaryotic Production and Community Structure in Offshore Mediterranean Waters

A dilution and size fractionation approach was used to study the separate and combined effects of viruses and flagellates on prokaryotic production ([(3)H]leucine incorporation) and community composition (16S rRNA gene PCR and denaturing gradient gel electrophoresis [DGGE]) in the upper mixed layer and the deep chlorophyll maximum in the offshore Mediterranean Sea. Four experiments were established using differential filtration: a resource control without predators (C treatment), treatment in the presence of viruses (V treatment), treatment in the presence of flagellates (F treatment), and treatment in the presence of both predators (VF treatment). The V and VF treatments increased prokaryotic abundance (1.4- to 2.3-fold) and the number of DGGE bands (by up to 43%) and decreased prokaryotic production compared to the level for the C treatment (by 22 to 99%). For the F treatment, significant differences compared to the level for the C treatment were found as well, but trends were not consistent across experiments. The relative abundances of the high-nucleic-acid subgroups of prokaryotes with high scatter (HNAhs) in flow cytometer settings were lower in the V and VF treatments than in the C and F treatments. These differences were probably due to lysis of very active HNA prokaryotes in the V and VF treatments. Our results indicate that the presence of viruses or viruses plus flagellates sustains prokaryotic diversity and controls prokaryotic production by regulating the proportion of the highly active members of the community. Our data also suggest that lysis and grazing control influences the relationship between bacterial community composition and prokaryotic production.

T1777 Decreased Ghrelin Response Mediates Upper Gastrointestinal Motility Disorder in Experimental GERD Rats

comprehensively characterize the presence and relative abundance of most known prokaryotes in a massively parallel assay. This unprecedented means of prokaryotic profiling provides the ability to elucidate microbial composition and the potential sources of inter-bowel and intra-bowel community heterogeneity as it relates to IBS. Aim: To assess the utility of the Phylochip to characterize and compare the large intestinal microbial communities between rats with an IBS-like phenotype (“IBS rats”) and healthy control rats. Methods: Neonatal rats underwent colonic exposure to dilute acetic acid or saline in an established paradigm. As adults, rats exposed to acetic acid demonstrate persistent colonic hypersensitivity and altered bowel movement. At 8-12 weeks, rats were euthanized and DNA was extracted and amplified separately from luminal and mucosal samples from the proximal, middle and distal colons. Results: PhyloChip analysis revealed that bacteria of the phyla Bacteroidetes, Firmicutes and Proteobacteria were the dominant organisms in both groups of rats. However, there were significant differences in the relative abundances of taxa at increasing levels of phylogenetic resolution. Preliminary data analysis has uncovered abrupt variations and disturbances in microbiota composition unique to IBS rats including altered species richness, changes in diversity and decreased abundance of certain taxa within specific regions of the large bowel. Principal component analysis (PCA) based on the UniFrac distance metric demonstrates that IBS microbiota is significantly different from the microbiota of controls. UniFrac analysis also demonstrates an orderly transition of bacterial communities from the proximal to the distal cecum in control rats, a pattern that was significantly disrupted in IBS rats. Conclusions.These initial findings suggest significant alterations in the colonic microbial community in an IBS model, findings that are supported by our concomitant comprehensive metabolomic analysis of these gut segments. These systems-based approaches, along with the availability of a suitable animal model, hold the promise of providing novel insight into the role of enteric microflora in IBS.

Impact of Silver Nanoparticle Contamination on the Genetic Diversity of Natural Bacterial Assemblages in Estuarine Sediments

Recent advancements in the nanotechnology industry have seen a growing interest in integrating silver nanoparticles (Ag-NPs) into consumer and medical products. To date, there has been little research into the toxicological impact that Ag-NPs will have when they enter the marine realm. Of particular concern are the possible effects of Ag-NPs on natural bacterial assemblages, given the antimicrobial activity of silver. In this study, estuarine sediment samples were dosed in triplicate for 20 days from a stock solution of Ag-NPs, with a final cumulative treatment of either 0 microg L(-1) (control), 25 microg L(-1) or 1000 microg L(-1). The experimental tanks were left for a further 10 days to allow for any recovery. Inductively coupled plasma-optical emission spectrometery (ICP-OES) of water and sediment samples confirmed that the Ag-NPs concentration in the aqueous phase decreased after each dosing and were transported to accumulate in the surface layer of the sediment (approximately top 3 mm). The overall concentration of Ag-NPs in the water column, however, increased steadily during the 20 days of dosing but decreased rapidly during the following 10 days without dosing. Nevertheless, the Ag-NPs did not have any impact on the prokaryotic abundance in the water column over the incubation period (ANOVA, P < 0.05). Environmental DNA was extracted from sediment samples and a two-step nested PCR-denaturing gradient gel electrophoresis (DGGE) approach, using PCR primers specific to the phylum Bacteria, was adopted to assess their diversity. Multivariate statistical analyses of presence/ absence matrices produced from DGGE profiles revealed negligible differences in bacterial diversity between treatments, suggesting that, under the selected experimental regime, Ag-NPs present little or no impact on estuarine sediment bacterial diversity. Possible reasons for this could include environmental factors, in particular the chloride ions in estuary water affecting the chemistry and behavior of Ag-NPs.

Short-term effect of oxic to anoxic transition on benthic microbial activity and solute fluxes in organic-rich phytotreatment ponds

Manipulative experiments to test the short-term effect of oxygen depletion events on microbial activity and benthic fluxes in organic-rich sediments were carried out in March and June 2004. Oxic-anoxic transitions were induced by prolonged dark incubation of sealed sediment cores collected in phytotreatment ponds. Benthic fluxes of oxygen (O2), carbon dioxide (CO2), inorganic nutrients, and free sulfides were measured before (oxic) and after (anoxic) the transition occurred. A multifactorial design was employed for monitoring esoenzymatic activity, heterotrophic bacterial production, total prokaryotic abundance, actively respiring bacterial cells, and the biochemical composition of sedimentary organic matter. The oxic to anoxic transition resulted in a significant increase of esoenzymatic activity and bacterial production in March, due to the profound modification of the benthic community and the release of labile organic compounds which followed the onset of anoxia. In parallel, net efflux rates of dissolved inorganic carbon (DIC) and ammonium (NH4 +) sharply decreased, soluble reactive phosphorus (SRP) influx reversed, and sulfide was buffered within the oxidized sediments. From March to June, ponds evolved toward oxygen deficit and reducing conditions in the upper sediment horizon, losing benthic fauna and biogeochemical buffering capacity. Thus, the oxic to anoxic transition had a much smaller effect on microbial activity and net flux exchange, while S2− was consistently delivered from the sediment to the water column. Overall data from this study suggest that the short-term response of benthic microbial activity and solute fluxes to anoxic events may have a significant impact on sediment biogeochemistry (e.g., at the oxic-anoxic interface), and that this impact may vary greatly depending on the sediment features, mainly its organic content and redox condition.

Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments

Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions.

Hydrolytic ectoenzyme activity associated with suspended and sinking organic particles within the anoxic Cariaco Basin

Ectohydrolase activities of suspended microbiota were compared to those associated with sinking particles (sed-POM) retrieved from sediment traps deployed in the permanently anoxic Cariaco Basin. In shore-based assays, activities of aminopeptidase, β-glucosidase, chitinase and alkaline phosphatase were measured in samples obtained from oxic and anoxic depths using MUF- and MCA-labeled fluorogenic substrate analogs. Hydrolysis potentials for these enzymes in the seston varied widely over the nine cruises sampled (8 Nov 1996–3 May 2000) and among depths (15–1265 m); from <10 to over 1600 nM d −1 hydrolysate released, generally co-varying with one another and with suspended particulate organic carbon (POC) and particulate nitrogen (PN). Hydrolytic potentials, prokaryotic abundances and POC/PN concentrations in sinking debris were 400–1.3×10 7 times higher than in comparable volumes of seawater. However when normalized to PN, hydrolytic potentials in sediment trap samples were not demonstrably higher than in Niskin bottle samples. We estimate that PN pools in sediment trap samples were turned over 2–1400 times (medians=7–26 x) slower by hydrolysis than were suspended PN pools. Median prokaryotic growth rates (divisions d −1) in sinking debris were also ∼150 times slower than for bacterioplankton. Hydrolytic potentials in surface oxic waters were generally faster than in underlying anoxic waters on a volumetric basis (nM hydrolysate d −1), but were not significantly ( p>0.05) different when normalized to PN or prokaryote abundances. Alkaline phosphatase was consistently the most active ectohydrolase in both sample types, suggesting that Cariaco Basin assemblages were adapted to decomposing phosphate esters in organic polymers. However, phosphorus limitation was not evident from nutrient inventories in the water column. Results support the hypothesis that efficiencies of polymer hydrolysis in anoxic waters are not inherently lower than in oxic waters.

Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes

Flooded rice paddy soils represent a typical anaerobic freshwater habitat of microorganisms. The abundance and community structure of sulfate reducing prokaryotes (SRP) were investigated in order to understand their response to different fertilization practices in rice paddy, including control without fertilizers (CT) and arrangements of different chemical fertilizers of nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK and NPK. The abundance of total bacteria and sulfate reducing prokaryotes of the rice paddy in summer and in winter were quantified by real-time PCR assays based on the 16S rRNA gene and the dissimilatory (bi)sulfite reductase gene ( dsrAB) β-subunit. No significant differences in the bacterial and SRP abundance were observed among different fertilization treatments in both winter and summer. The mean copy numbers of bacteria was 7.26 × 10 9 copies g −1 dry soil in winter and 1.27 × 10 10 copies g −1 dry soil in summer. The average dsrAB gene copy numbers of the SRP was 5.08 × 10 8 copies g −1 dry soil in winter and 5.92 × 10 8 copies g −1 dry soil in summer. The dsrAB gene clone libraries of the five fertilization treatments were constructed and their RFLP analysis yielded 22–25 restriction patterns, suggesting a high degree of dsrAB sequence diversity in different fertilization treatments. There was no significant change in the soil SRP community structure among the different fertilization regimes. More than half of the sequences were affiliated with novel branching clusters which were uncultured SRP. Clostridia and Deltaproteobacteria were also found with a high proportion in the clone libraries, while Desulfovibrionaceae was absent. High proportion of novel uncultured SRP implies that they may play important roles in paddy soils and deserve further studies.