Roseobacter-Like Bacteria in Red and Mediterranean Sea Aerobic Anoxygenic Photosynthetic Populations

Bacteriochlorophyll a-containing aerobic anoxygenic phototrophs (AAnP) have been proposed to account for up to 11% of the total surface water microbial community and to potentially have great ecological importance in the world's oceans. Recently, environmental and genomic data based on analysis of the pufM gene identified the existence of α-proteobacteria as well as possible γ-like proteobacteria among AAnP in the Pacific Ocean. Here we report on analyses of environmental samples from the Red and Mediterranean Seas by using pufM as well as the bchX and bchL genes as molecular markers. The majority of photosynthesis genes retrieved from these seas were related to Roseobacter-like AAnP sequences. Furthermore, the sequence of a novel photosynthetic operon organization from an uncultured Roseobacter-like bacterial artificial chromosome retrieved from the Red Sea is described. The data show the presence of Roseobacter-like bacteria in Red and Mediterranean Sea AAnP populations in the seasons analyzed.     

Biodiversity of benthic invertebrates and organic matter processing in shallow marine sediments: an experimental study

The main objective of this study was to measure the impact of benthic invertebrate diversity on processes occurring at the water-sediment interface. We analyzed the effects of interactions between three shallow water species (Cerastoderma edule, Corophium volutator, and Nereis diversicolor). The impacts of different species richness treatments were measured on sediment reworking, bacterial characteristics, and biogeochemical processes (bromide fluxes, O₂ uptake, nutrient fluxes, and porewater chemistry) in sediment cores. The results showed that the three species exhibited different bioturbation activities in the experimental system: C. edule acted as a biodiffusor, mixing particles in the top 2 cm of the sediments; C. volutator produced and irrigated U-shaped tubes in the top 2 cm of the sediments; and N. diversicolor produced and irrigated burrow galleries in the whole sediment cores. C. edule had minor effects on biogeochemical processes, whereas the other species, through their irrigation of the burrows, increased the solute exchange between the water column and the sediment two-fold. These impacts on sediment structure and solute transport increased the O₂ consumption and the release of nutrients from sediments. As N. diversicolor burrowed deeper in the sediment than C. volutator, it irrigated a greater volume of sediments, with great impact on the sediment cores.Most treatments with a mixture of species indicated that observed values were often lower than predicted values from the addition of the individual effects of each species, demonstrating a negative interaction among species. This type of negative interaction measured between species on ecosystem processes certainly resulted from an overlap of bioturbation activities among the three species which lived and foraged in the same habitat (water-sediment interface). All treatments with N. diversicolor (in isolation and in mixture) produced similar effect on sediment reworking, water fluxes, nutrient releases, porewater chemistry, and bacterial characteristics. Whichever species associated with N. diversicolor, the bioturbation activities of the worm hid the effect of the other species. The results suggest that, in the presence of several species that use and modify the same sediment space, impact of invertebrates on ecosystem processes was essentially due to the most efficient bioturbator of the community (N. diversicolor). In consequence, the functional traits (mode of bioturbation, depth of burrowing, feeding behaviour) of an individual species in a community could be more important than species richness for some ecosystem processes.     

Classification of <Emphasis Type="Italic">Rhizoctonia</Emphasis> spp. using rDNA-ITS sequence analysis supports the genetic basis of the classical anastomosis grouping

Currently, rDNA-ITS sequence analysis seems to be the most appropriate method for comprehensive classification of Rhizoctonia spp. Our previous review article was concerned with detailed analysis of multinucleate Rhizoctonia (MNR), and the current review complements the previous one with detailed analysis of binucleate Rhizoctonia (BNR) (teleomorphs: Ceratobasidium spp. and Tulasnella spp.) and uninucleate Rhizoctonia (UNR) (teleomorph: C. bicorne). Data of all the appropriate BNR and UNR accumulated in GenBank were analyzed together in neighbor-joining (NJ) trees supplemented with percent sequence similarity within and among the anastomosis groups (AGs) and subgroups. Generally, the clusters of the isolate sequences supported the genetic basis for the AG based on hyphal fusion anastomosis. Comprehensive interrelationships among all the currently available MNR, BNR, and UNR groups and subgroups in GenBank were subsequently analyzed in NJ and maximum-parsimony (MP) trees, showing the genetic relatedness among the different groups and indicating possible bridging groups between MNR, BNR, and UNR. The review also indicates serious inaccuracies in designation of sequences of some isolates deposited in GenBank. Several additional teleomorph genera with Rhizoctonia spp. anamorphs have also been reported in the literature. However, as they have not been intensively studied, there were no available data on their rDNA-ITS sequences that could be included in this review.     

Comparative understanding of UTS2 and UTS2R genes for their involvement in type 2 diabetes mellitus

Several reports have shown that urotensin 2 (UTS2) and its receptor (UTS2R) are involved in glucose metabolism and insulin resistance, which lead to development of type 2 diabetes mellitus (T2DM) in humans. In the present study, we annotated both bovine UTS2 and UTS2R genes and identified 5 single nucleotide polymorphisms (SNPs) for the former gene and 14 mutations for the latter gene. Four mutations were genotyped on a Wagyu x Limousin reference population, including 6 F₁ bulls, 113 F₁ dams and ~250 F₂ progeny. Among 12 phenotypes related to fat deposition and fatty acid composition, we observed that the UTS2 gene was significantly associated with the amount of skeletal saturated fatty acids, while its receptor (UTS2R) gene had significant effects on amounts of saturated and monounsaturated fatty acids, Δ⁹ desaturase activity for converting 16:0 into 16:1, muscle fat (marbling) score and Longissimus Dorsi muscle area. However, in this population, these markers were not associated with subcutaneous fat depth or percent kidney, pelvic and heart fat. We also found that mutations in the promoter regions altered the promoter activities in both genes and coding SNPs might affect the mRNA stability in the UTS2R gene. Overall, our present study provides the first evidence that both UTS2 and UTS2R genes regulate skeletal muscle fat accumulation and fatty acid metabolism, thus indicating their potential pathological functions related to obesity and T2DM in humans.     

Genome Assembly Anchored QTL Map of Bovine Chromosome 14

Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 – 10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb - 73.84 Mb and 7.86 Mb – 39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb – 45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle.