Predation and respiration by the small cyclopoid copepod Oithona similisr: How important is feeding on ciliates and heterotrophic flagellates?

Feeding on natural plankton populations and respiration of thesmall cyclopoid copepod Oithona similis were measured duringthe warm season in Buzzards Bay, Massachusetts, USA. AlthoughO.similis did not significantly ingest small autotrophic andheterotrophic flagellates (2–8 µn), this copepodactively fed on >10 µm particles, including autotrophic/heterotrophic(dino)flagel-lates and ciliates, with clearance rates of 0.03–0.38ml animal^–1 h^–1. The clearance rates increased withthe prey size. O.similis also fed on copepod nauplii (mainlycomposed of the N1 stage of Acartia tonsa with a clearance rateof 0.16 ml animal^–1 h^–1. Daily carbon ration fromthe combination of these food items averaged 148 ng C animal^–1day^–1 (41% of body C day^–1), with ciliates and heterotrophicdino-flagellates being the main food source ({small tilde}69%of total carbon ration). Respiration rates were 020–0.23µl O₂ animal^–1 day^–1. Assuming a respiratoryquotient of 0.8 and digestion efficiency of 0.7, the carbonrequirement for respiration was calculated to be 125–143ng C animal^–1 day^–1, close to the daily carbon rationestimated above. We conclude that predation on ciliates andheterotrophic dinoflagellates was important for O.similis tosustain its population in our study area during the warm season.     

Influence of wastewater treatment on the microbial ecology of a large, temperate river system — the Danube River

In an attempt to assess the influence of tertiary-treated sewage influx on bacterial metabolism in the Danube River, bacterial abundance, ectoenzymatic activity, faecal coliforms, faecal streptococci, chlorophyll a (chl a), concentrations of dissolved (DOC) and total organic carbon (TOC) and inorganic nutrients were measured upstream of the sewage influx and compared with sampling sites downstream. Additional samples were taken near the outlet of the sewage treatment plant. Bacterial abundance as determined by epifluorescence microscopy was compared with plate counts of total heterotrophic bacteria. Significantly higher values were obtained at the stations downstream from the sewage influx only for faecal coliforms and faecal streptococci, for glucuronidase activity and bacterial biovolume. All the other parameters were not significantly different from values obtained at the upstream sampling site. Strong seasonal dependence was detectable for nitrate with high concentrations during the winter ( 250 µM) and low concentrations during summer ( 100 µM). A distinct spring phytoplankton bloom was noticeable in the river reaching chl a concentrations of 70 µg 1^–1; during the remaining seasons chl a concentrations were <20 µg 1^–1. Highly significant correlations were found between faecal coliform counts and glucuronidase activity. C:N:P ratios of 13.9:10.7:1 (for the upstream station) and 11.7:9.2:1 (for the downstream stations) of dissolved nutrients are rather low indicating severe carbon limitation of bacterioplankton. Based on our results we conclude that the heterotrophic bacterial community is not significantly effected by the input of treated sewage but faecal contamination is readily detectable over a comparatively long reach of 30 km.     

Translation attenuation regulation of chloramphenicol resistance in bacteria — a review

The chloramphenicol (Cm)-inducible cat and cmlA genes are regulated by translation attenuation, a regulatory device that modulates mRNA translation. In this form of gene regulation, translation of the Cm^R coding sequence is prevented by mRNA secondary structure that sequesters its ribosome-binding site (RBS). A translated leader of nine codons precedes the secondary structure, and induction results when a ribosome becomes stalled at a specific site in the leader. Here we demonstrate that the site of ribosome stalling in the leader is selected by a cis effect of the nascent leader peptide on its translating ribosome.     

Isopropylbenzene (cumene) — a new substrate for the isolation of trichloroethene-degrading bacteria

Various bacterial isolates from enrichments with isopropylbenzene (cumene), toluene or phenol as carbon and energy sources were tested as to their potential to oxidize trichloroethene (TCE). In contrast to toluene and phenol, all isolates enriched on isopropylbenzene were able to oxidize TCE. Two isolates, strain JR1 and strain BD1, were identified as Pseudomonas spec. and as Rhodococcus erythropolis, respectively. TCE oxidation was accompanied by the liberation of stoichiometric amounts of chloride. Initial TCE oxidation rate increased proportional to the substrate concentration from 25 to 200 M TCE. Maximal initial TCE-degradation rates found here were 4 to 5 nmol · min^-1 · mg protein^-1. The TCE degradation rate decreased with time. The two isolates showed a temperature optimum for TCE degradation between 10 and 20 °C. In addition to TCE, R. erythropolis BD1 degraded only cis- and trans-dichloroethene whereas Pseudomonas spec. JR1 was able to oxidize also 1,1-dichloroethene, vinyl chloride, trichloroethane, and 1,2-dichloroethane.Abbrevations DMF dimethylformamide - TCE trichloroethene     

“Biofilmology”: a multidisciplinary review of the study of microbial biofilms

The observation of biofilm formation is not a new phenomenon. The prevalence and significance of biofilm and aggregate formation in various processes have encouraged extensive research in this field for more than 40 years. In this review, we highlight techniques from different disciplines that have been used to successfully describe the extracellular, surface and intracellular elements that are predominant in understanding biofilm formation. To reduce the complexities involved in studying biofilms, researchers in the past have generally taken a parts-based, disciplinary specific approach to understand the different components of biofilms in isolation from one another. Recently, a few studies have looked into combining the different techniques to achieve a more holistic understanding of biofilms, yet this approach is still in its infancy. In order to attain a global understanding of the processes involved in the formation of biofilms and to formulate effective biofilm control strategies, researchers in the next decade should recognise that the study of biofilms, i.e. biofilmology, has evolved into a discipline in its own right and that mutual cooperation between the various disciplines towards a multidisciplinary research vision is vital in this field.     

Cyanobacterium Nostoc paludosum Kütz as a basis of creation of agriculturally useful microbial associations by the example of bacteria of the genus Rhizobium

Different species of Rhizobium were successfully introduced into the extracellular slime of Nostoc paludosum (Kütz) Elenk, strain 18; cyanobacteria did not eliminate them and exhibited no specificity to the introduced species. Both partners were shown to exist in a self-sufficient manner in an artificial consortium, the stability of which is determined by the technology of growing the cultures in collections. Cyanobacteria act as carriers of introduced satellites, providing contact with the inoculated material through the slime, and increase the nitrogen-fixing ability of legume plants due to the increase of the number and activity of nodules. The fact of penetration of cyanobacterial hormogonia into the nodules has been noted. The treatment of seeds by the consortium resulted in an increase of the harvest as compared with the standard methods of nitragin treatment of legumes.     

A comparison of the refractile bodies (R-bodies) of certain bacteria—II. Effects of pH on the structure

The ‘R-bodies’ of Caedibacter taeniospiralis, an endosymbiont of Paramecium tetraurelia and Pseudomonas avenae, have been examined under a wide range of pH. They both unroll over a small range, but in both cases the process does not always proceed to completion. Acid pHs cause both to unroll. All the R-bodies of P. avenae at high pHs are wound which is not the case with Caedibacter. There are differences between the two bodies in the details of their unrolling. Caedibacter taenospiralis unwinds from the inside, whereas P. avenae unwinds from the outside. Detailed study of the unwound ribbon shows a difference in terms of roughness and smoothness of the two surfaces.     

Food additives,contaminants and other minor components: effects on human gut microbiota—a review

Gut bacteria play an important role in several metabolic processes and human diseases, such as obesity and accompanying co-morbidities, such as fatty liver disease, insulin resistance/diabetes, and cardiovascular events. Among other factors, dietary patterns, probiotics, prebiotics, synbiotics, antibiotics, and non-dietary factors, such as stress, age, exercise, and climatic conditions, can dramatically impact the human gut microbiota equilibrium and diversity. However, the effect of minor food constituents, including food additives and trace contaminants, on human gut microbiota has received less attention. Consequently, the present review aimed to provide an objective perspective of the current knowledge regarding the impacts of minor food constituents on human gut microbiota and consequently, on human health.     

Oligochaeta of the Danube River — a faunistical review

The aim of this work is to discuss the distribution of Oligochaeta (Annelida) in the Danube River using the collections made by the Joint Danube Survey 2007 (JDS2) on more than 2800 km of the river. The basic faunistical features of the oligochaete assemblages were analysed with regard to three main sectors of the Danube (upper, middle and lower reaches, the last with the Danube Delta). A total of 52 oligochaete taxa have been recorded. Most of the observed species are typical of the potamon-type rivers in the region, and are well adapted to moderate-to-high organic load. The highest taxa richness and frequency of occurrence were observed among the Tubificidae family. Naididae, Propappidae, Enchytraeidae and Haplotaxidae had also low frequency. The upper reach of the Danube showed the lowest species richness, while the middle reach is characterised by its highest species richness. Construction of dams and regulation of the riverbed have resulted in an increase of limno(rheo)philic taxa which prefer slow-flowing and lentic zones.     

“Candidatus Sonnebornia yantaiensis”, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora,Oligohymenophorea)

An intracellular bacterium was discovered in an isolate of Paramecium bursaria from a freshwater pond in Yantai, China. The bacteria were abundant and exclusively found in the cytoplasm of the host which, along with the green alga Chlorella, formed a three-partner consortium that could survive in pure water for at least one week. Cloning, sequencing and phylogenetic analysis of the bacterial 16S rRNA gene showed that the bacterium belonged to the uncultured candidate division OD1, which usually forms part of the rare biosphere. Transmission electron microscopy and fluorescence in situ hybridization (FISH) with specific probes showed that the bacteria were usually located close to the perialgal membranes of endosymbiotic Chlorella cells, and occasionally irregularly distributed throughout the host cytoplasm. The name “Candidatus Sonnebornia yantaiensis” gen. nov., sp. nov. is proposed for the new bacterium. A strongly supported monophyletic subclade, OD1-p, which included the new species, was recognized and this study highlights that protists can be important hosts for rare bacterial taxa.     

Effect of N,N′-bis (alkyldimethyl)-α,ω-alkanediammonium dibromides on bacteria of the genusclostridium

Antibacterial effect of 17 ammonium compounds of the type of N,N′-bis(alkyldimethyl)-α,ω-alkanediammonium dibromides was tested on anaerobically sporulating bacteria of the genusClostridium. A sizable antibacterial activity was displayed by five N,N′-bis(alkyldimethyl)-1,6-hexanediammonium dibromides and by four N,N′-bis(decyldimethyl)-α,ω-alkanediammonium dibromides. These compounds exhibited activity higher than, or comparable with, that of the reference standards Ajatin and Septonex. The maximum antibacterial activity was found in compounds whose alkyl chain contained 9–12 carbon atoms. Compounds with a lower number of carbon atoms in the chain (less than 8) exhibited a low activity.     

Formation of symbiotic communities of ciliates,algae, and cyanobacteria in a waterbody of the Ptich’ya Gavan nature park (Omsk)

This article deals with the formation of symbiotic communities in a waterbody of the Ptich’ya Gavan nature park (Omsk) at the end of May 2010. The samples were collected by plankton nets, fixed in formalin, and examined with the use of optical microscope. The symbiotic communities consist of ciliates Ophrydium versatile and 35 other species and forms of algae and cyanobacteria inhabiting the pelagic zone of the waterbody. It is found that the species composition of producers in these communities is formed as a result of the higher adaptation of some species to specific conditions regardless of their abundance. The species with high tolerance to abiotic environmental factors (cosmopolitan species), inhabitants of polluted zones, and species with high tolerance to the concentrations of organic matter in water are most abundant.     

Variation of a benthic heterotrophic bacteria community with different respiratory metabolisms in Coyuca de Benítez coastal lagoon (Guerrero, Mexico)

The fluctuations of the number, biomass and composition of the heterotrophic community were studied daily for two days, according to depth, pH, Eh, O2 and organic carbon concentration within a zone of the canal between the Coyuca de Benitez lagoon (Guerrero, Mexico) and the coastal waters. At the three moments of the day studied (6 am, 2 pm and 10 pm), the oxygen concentrations in the overlying water and in the superficial sediment layer were near air-saturation in the diurnal samplings (582 microM at 6 am and 665 microM at 2 pm), and sub-satured during the night (158 microM). In the sediments, the models of vertical distribution of Eh and organic carbon distributions were very irregular due to the bio-perturbation of the benthic, meio- and macrofauna, whose activity allows the superficial organic carbon to migrate towards sediment deeper layers. Vertical distribution of the different viable bacteria populations seems to be related to the hydrodynamic patterns of the communicating canal and sediments heterogeneity. In the sediment column, the heterotrophic bacteria total number varied from 6.8 to 20.3 x 108 cells cm(-3). The highest heterotrophic bacterial biomass values were encountered during the diurnal samplings (39.2 microgC.l(-1) at 6 am and 34.4 microgC.(l(-1) at 2 pm) and the lowest during the night (9.7 microgC.l(-1). The fluctuations of viable heterotrophic bacteria populations with different respiratory metabolisms (aerobic, microaerophilic and anaerobic) can be explained by the existence of suboxic microniches that appear when particles of sediment are resuspended due to the water circulation and the benthic infauna excavating activity, that allows the supernatant water oxygen to penetrate through its galleries towards deeper sediment zones. The statistical analysis (Multiple lineal regression model r2 > or = 0.5) showed that the on the whole, the hydrological parameters are not influence over the bacterial number and bacterial biomass distribution (r2 < or = 0.5), Nevertheless, the variations of the heterotrophic bacteria community observed in the two days sampling, seem to be governed (with F-values of 0.6 to 0.9) by the irregular flows of bio-available organic material and the sediment porosity.     

Visual ecology of aphids—a critical review on the role of colours in host finding

We review the rich literature on behavioural responses of aphids (Hemiptera: Aphididae) to stimuli of different colours. Only in one species there are adequate physiological data on spectral sensitivity to explain behaviour crisply in mechanistic terms. Because of the great interest in aphid responses to coloured targets from an evolutionary, ecological and applied perspective, there is a substantial need to expand these studies to more species of aphids, and to quantify spectral properties of stimuli rigorously. We show that aphid responses to colours, at least for some species, are likely based on a specific colour opponency mechanism, with positive input from the green domain of the spectrum and negative input from the blue and/or UV region. We further demonstrate that the usual yellow preference of aphids encountered in field experiments is not a true colour preference but involves additional brightness effects. We discuss the implications for agriculture and sensory ecology, with special respect to the recent debate on autumn leaf colouration. We illustrate that recent evolutionary theories concerning aphid–tree interactions imply far-reaching assumptions on aphid responses to colours that are not likely to hold. Finally we also discuss the implications for developing and optimising strategies of aphid control and monitoring.     

A review on the occurrence and taxonomy of heterotrophic protists in extreme acidic environments of pH values ≤ 3

The occurrence and some important taxonomic problems of heterotrophic protists from extremely acidic (pH 3) environments are briefly discussed. Almost all information on the occurrence of heterotrophic protists from extremely acidic environments is restricted to acid mine drainage (AMD) or streams influenced by AMD. Most of the information is provided for ciliates. Very little information is available on the occurrence of flagellates, rhizopods and heliozoa in this environment. Within the ciliates Urotricha, Vorticella and Oxytricha dominate in acidic mining lakes. Actinophrys sp. is the most important heliozoan in these environments. There are many taxonomic problems which are not solved so far. Live observations and taxonomic methods adapted to the extreme chemical matrix are necessary for correct identification.     

In silico evidence for the horizontal transfer of gsiB, a σ(B)-regulated gene in gram-positive bacteria, to lactic acid bacteria

gsiB, coding for glucose starvation-inducible protein B, is a characteristic member of the σ(Β) stress regulon of Bacillus subtilis and several other Gram-positive bacteria. Here we provide in silico evidence for the horizontal transfer of gsiB in lactic acid bacteria that are devoid of the σ(Β) factor.     

Flashback and foreshadowing—a review of the taxon Opisthobranchia

Opisthobranchia have experienced an unsettled taxonomic history. At the moment their taxonomy is in state of dramatic flux as recent phylogenetic studies have revealed traditional Opisthobranchia to be paraphyletic or even polyphyletic, allocating some traditional opisthobranch taxa to other groups of Heterobranchia, e.g. Pulmonata. Here we review the history of Opisthobranchia and their subgroups, explain their traditionally proposed relationships, and outline the most recent phylogenetic analyses based on various methods (morphology, single gene and multiple gene analyses, as well as genomic data). We also present a phylogenetic hypothesis on Heterobranchia that, according to the latest results, represents a consensus and is the most probable one available to date. The proposed phylogeny supports the Acteonoidea outside of monophyletic Euthyneura, the basal euthyneuran split into Nudipleura (Nudibranchia plus Pleurobranchoidea) and the recently established taxon Tectipleura. The latter divides into the Euopisthobranchia, containing most of the major traditional opisthobranch clades, and the Panpulmonata, with a mix of the former opisthobranch, putative allogastropod and pulmonate taxa. This “new euthyneuran tree” rejects the traditional taxa Opisthobranchia and Pulmonata, and, in particular, has profound implications for preconceived textbook scenarios of opisthobranch and pulmonate evolution, which must now be reconsidered. In the absence of systematic barriers, research communities—which have traditionally investigated marine and non-marine heterobranchs separately—need to interact and finally merge for the sake of science.     

Towards a phylogeny of phototrophic purple sulfur bacteria — the genus Ectothiorhodospira

While most strains of heterofermentative lactobacilli and strains of Leuconostoc species contained only traces of a dehydratase reacting with glycerol or propanediol-1,2, three strains of Lactobacillus brevis and one strain of L. buchneri that metabolized glycerol readily in the presence of glucose, contained propanediol-1,2 dehydratase (EC 4.2.1.28). This cobamide requiring enzyme from L. brevis B 18 was partially purified. It reacts with the substrates propanediol-1,2, glycerol and ethanediol-1,2 with the relative activities of about 3:2:1. This ratio remained unchanged throughout the purification procedure. The substrate affinities were measured: propanediol-1,2 K _m=0.6 mM, glycerol K _m=4 mM, ethanediol-1,2 K _m=5.3 mM coenzyme B₁₂ (substrate glycerol) K _m=0.007 mM. The activity of the dehydratase was promoted by potassium or ammonium ions and inhibited by sodium, lithium, magnesium or specially manganese. The apparent molecular weight of propanediol-1,2 dehydratase was determined as M_r=180,000.Dedicated to Prof. Dr. H. G. Schlegel on behalf of his 60th birthday     

The effect of epibenthic predators and macroalgal cover on the benthic macroinvertebrate community of a shallow lagoon in the Bay of Cádiz (SW Spain)

Three field predator exclusion experiments were conducted in 1992 on a lagoonal muddy pan of the Bay of Cádiz to measure the effects of large epibenthic predators (fish and crustacean decapods) on the benthic macroinvertebrate community at different periods of the year (May–June, August–September, November–December). At the end of each field experiment (30–31 days), benthic macrofaunal communities within exclosures and control plots (three replicates for each treatment) were compared. There were no considerable exclosure artifacts in all three experiments, but a great heterogenity in the spatial macrofaunal distribution was observed especially in the late autumn experiment. No systematic change in overall faunal characteristics was observed with the exclusion of epibenthic predators, except significantly greater mean individual sizes (all experiments) and lower total densities (June and December) within exclosures. For several benthic species, a statistically detectable increased density and larger mean individual size were also observed within exclosures in May–June and August–September experiments but not in December, probably related to the higher predatory activity during the warm season. Conversely, the amphipod Microdeutopus gryllotalpa showed lower density but also larger mean size when epibenthic predators were excluded. An algal cover (Ulva) was present at three field experiments and had a mixed effect on the density of benthic macrofauna. Some epifaunal species (or epifaunal stages) were positively affected by the algal biomass, while some infaunal species were negatively affected.