Bioavailability of organic matter in a freshwater estuarine sediment: long<Emphasis Type="Bold">-</Emphasis>term degradation experiments with and without nitrate supply

Organic carbon degradation experiments were carried out using flow-through reactors with sediments collected from an intertidal freshwater marsh of an eutrophic estuary (The Scheldt, Belgium). Concentrations of nitrate, nitrite, dissolved inorganic carbon (DIC), dissolved organic carbon, methane, dissolved cations (Ca²⁺, Mg²⁺, Na⁺ and K⁺), total dissolved Fe, phosphate and alkalinity were measured in the outflow solutions from reactors that were supplied with or without the terminal electron acceptor nitrate. Organic carbon mineralization rates were computed from the release rates of DIC after correcting for the contribution of carbonate mineral dissolution. The experiments ran for several months until nitrate reducing activity could no longer be detected. In the reactors supplied with nitrate, 10–13% of the bulk sedimentary organic carbon (SOC) was mineralized by the end of the experiments. In reactors receiving no nitrate, only 3–9% of the initial SOC was mineralized. Organic matter utilization by nitrate reducers could be described as the simultaneous degradation of two carbon pools with different maximum oxidation rates and half-saturation constants. Even when nitrate was supplied in non-limiting concentrations about half of the carbon mineralization in the reactors was due to fermentative processes, rather than being coupled to nitrate respiration. Fermentation may thus be responsible for a large fraction of the DIC efflux from organic-rich, nearshore sediments.     

Nitrogen and Phosphorus Limitation of Phytoplankton Growth in New Zealand Lakes: Implications for Eutrophication Control

We examine macronutrient limitation in New Zealand (NZ) lakes where, contrary to the phosphorus (P) only control paradigm, nitrogen (N) control is widely adopted to alleviate eutrophication. A review of published results of nutrient enrichment experiments showed that N more frequently limited lake productivity than P; however, stoichiometric analysis of a sample of 121 NZ lakes indicates that the majority (52.9%) of lakes have a mean ratio of total nitrogen (TN) to total phosphorus (TP) (by mass) indicative of potential P-limitation (>15:1), whereas only 14.0% of lakes have mean TN:TP indicative of potential N-limitation (<7:1). Comparison of TN, TP, and chlorophyll a data between 121 NZ lakes and 689 lakes in 15 European Union (EU) countries suggests that at the national scale, N has a greater role in determining lake productivity in NZ than in the EU. TN:TP is significantly lower in NZ lakes across all trophic states, a difference that is driven primarily by significantly lower in-lake TN concentrations at low trophic states and significantly higher TP concentrations at higher trophic states. The form of the TN:TP relationship differs between NZ and the EU countries, suggesting that lake nutrient sources and/or loss mechanisms differ between the two regions. Dual control of N and P should be the status quo for lacustrine eutrophication control in New Zealand and more effort is needed to reduce P inputs.     

Are Water Beetles Good Indicators of Biodiversity in Mediterranean Aquatic Ecosystems? The Case of the Segura River Basin (SE Spain)

Water beetles were examined for use as potential biodiversity indicators in continental aquatic ecosystems in a semiarid Mediterranean region, the Segura river basin (SE Spain). The indicator value of water beetles was investigated by examining the degree to which their species richness patterns was correlated with other groups (Plecoptera, Trichoptera, Mollusca, Heteroptera and Ephemeroptera), and the efficiency of water beetle area networks (selected by complementarity) in conserving overall groups richness. The species richness patterns of Coleoptera, Ephemeroptera, Plecoptera and Trichoptera were significantly correlated with the Remaining Richness value (RR), defined as the total number of species found at a site (of all six groups examined) minus the number of species belonging to the considered indicator group. Area networks for Coleoptera selected by complementarity represented the highest RR percentage (84.46%) and contained more than 78% species of each group. Furthermore, water beetles meet most of the criteria proposed in the literature for choosing biodiversity indicator taxa. In our study, the correlation values and the percentage of species represented by family, genus and species complementary networks were similar and we suggest that the higher taxa of water beetles (genera or families) can be used as biodiversity surrogates for cost-effective practical surveys.     

Metagenomic analysis of the viral communities in fermented foods

Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral order Caudovirales (i.e., Myoviridae, Podoviridae, and Siphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.     

Assessing Gut Microbial Diversity from Feces and Rectal Mucosa

Gut microbiota is the most complex bacterial community in the human body and its study may give important clues to the etiology of different intestinal diseases. Most studies carried out so far have used fecal samples, assuming that these samples have a similar distribution to the communities present throughout the colon. The present study was designed to test this assumption by comparing samples from the rectal mucosa and feces of nine healthy volunteers by sequencing libraries of 16S rRNA genes. At the family taxonomic level, where rarefaction curves indicate that the observed number of taxa is close to the expected one, we observe under different statistical analyses that fecal and mucosal samples cluster separately. The same is found at the level of species considering phylogenetic information. Consequently, it cannot be stated that both samples from a given individual are of similar composition. We believe that the evidence in support of this statement is strong and that it would not change by increasing the number of individuals and/or performing massive sequencing. We do not expect clinicians to stop using feces for research, but we think it is important to caution them on their potential lack of representativeness with respect to the bacterial biofilm on the rectal mucosa.     

Hydrology is reflected in the functioning and community composition of methanotrophs in the littoral wetland of a boreal lake

In lake ecosystems a major proportion of methane (CH(4) ) emissions originate from the littoral zone, which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands have been poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyse spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kev?t?n, Eastern Finland). The wetland had a hydrology gradient with a mean water table varying from -8 to -25 cm. The wettest area, comprising the highest CH(4) oxidation, had the highest abundance and species richness of methanotrophs. A high water table favoured the occurrence of type Ib methanotrophs, whereas types Ia and II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on the water table, which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity and diversity of methanotrophs, and consequently CH(4) emissions from such systems.     

The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function σ factors

Extracytoplasmic function (ECF) σ factors are critical players in signal transduction networks involved in bacterial response to environmental changes. The Myxococcus xanthus genome reveals ～45 putative ECF‐σ factors, but for the overwhelming majority, the specific signals or mechanisms for selective activation and regulation remain unknown. One well‐studied ECF‐σ, CarQ, binds to its anti‐σ, CarR, and is inactive in the dark but drives its own expression from promoter P_QRS on illumination. This requires the CarD/CarG complex, the integration host factor (IHF) and a specific CarD‐binding site upstream of P_QRS. Here, we show that DdvS, a previously uncharacterized ECF‐σ, activates its own expression in a CarD/CarG‐dependent manner but is inhibited when specifically bound to the N‐terminal zinc‐binding anti‐σ domain of its cognate anti‐σ, DdvA. Interestingly, we find that the autoregulatory action of 11 other ECF‐σ factors studied here depends totally or partially on CarD/CarG but not IHF. In silico analysis revealed possible CarD‐binding sites that may be involved in direct regulation by CarD/CarG of target promoter activity. CarD/CarG‐linked ECF‐σ regulation likely recurs in other myxobacteria with CarD/CarG orthologous pairs and could underlie, at least in part, the global regulatory effect of the complex on M. xanthus gene expression.     

Costs of reproduction in male lizards, Sceloporus virgatus

Models of life history evolution typically assume a balance between the benefits of current reproductive activity and the costs to future reproductive success or survivorship, but empirical studies often find positive correlations between such components of fitness in undisturbed animal populations. I examined possible survivorship costs of reproduction in free-ranging male lizards, Sceloporus virgatus , and found that males with low levels of mating success were less likely to survive to the following breeding season. I also investigated two possible indicators of reproductive effort, increase in ectoparasite load and decrease in body weight during the breeding season. Levels of parasitism with trombiculid mites at the end of the breeding season were not associated with any measure of fitness or body condition (mating success, survivorship to the following year, relative weight loss). Yearling males (which have low levels of mating success) usually gained weight during the breeding season, while older males generally lost weight during this period. This suggests that young males may have postponed reproduction in favor of body growth and that seasonal weight loss of older males might reflect reproductive effort. Within the group of older males, individuals with the highest levels of mating success did not have high levels of either weight loss or mortality. Mate guarding behavior, an alternative to the aggressive territorial behavior typical of many lizard species, may allow certain males to obtain mates without expending large amounts of energy or exposing themselves to great mortality risks.