Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.)

In a previous study, we found that the growth performance of the new strain of Huanghe carp is related to gene expression and bacterial community in the gut. In order to better understand the relationship between the gene expression level and bacterial abundance in the gut, we studied the growth performance, gut bacterial structure, and transcriptome profile in the 4th generation of the new carp strain (selection group) at harvesting time, and compared them with the control line (traditional Huanghe carp). Body weight, depth, width, and length increased 14.58, 7.14, 5.04, and 5.07%, respectively. The gut microbiome of the selection group also exhibited significantly higher species diversity parameters (Shannon, Simpson, and chao1). Both PCA and phylogenetic analyses divided all gut samples into two parts: control and selection group. Aeromonas was the dominant taxon in the control group, followed by Firmicutes and Roseomonas; in the selection group, Roseomonas was the dominant taxon, followed by Firmicutes and then Aeromonas. Among the 249 significantly differentially expressed genes, 194 were downregulated and 55 were upregulated. Functional GO annotation produced 13 terms in the biological process, 8 in the cellular component, and 7 in the molecular function categories. KEGG annotation indicated that most of these genes were associated with the immune-related pathways. A total of 2,892 pairs of genes (245) and baceterial genera (256) were analyzed using Pearson’s correlation analysis. Most of the identified associations were mapped to the immune system, bacterial community, and cell differentiation categories. The top-10 bacterial genera identified by these analyses were Methylocystis, Ohtaekwangia, Roseomonas, Shewanella, Lutispora, GpVI, Desulfovibrio, Candidatus_Berkiella, Bordetella, and Azorhizobium. Genes paired with bacteria flora were divided into four functional categories: immune, growth, adipocyte differentiation, and nerve regulation. These genes may be related to the comparatively fast growth and high muscle polyunsaturated fatty acid content of the Huanghe carp new strain. Meanwhile, nerve regulation-related genes may be a reflection of the microbiota-gut-brain axis. These results illustrate that gut bacterial community structure is associated with the growth performance and gene expression in the Huanghe carp new strain.

Effects of Oat Hay Content in Diets on Nutrient Metabolism and the Rumen Microflora in Sheep

Oats have the characteristics of drought tolerance, cold resistance, strong adaptability, high forage yield, and high nutritional value. However, there are few reports on the most appropriate amount of oat hay in ruminant diets, the digestion and metabolism of ruminants, and the rumen microflora. To study the effects of oat hay content in diets on nutrient digestion and metabolism and the rumen microflora in sheep, 9 German Merino and Mongolian crossbred rams of similar body condition and weight with permanent fistulas were selected. The 3 × 3 Latin square design was used to randomly divide the rams into 3 groups, with 3 animals in each group. The three groups were fed different kinds of roughage: whole-plant corn silage only (corn silage group, CSG), oat hay mixed with whole-plant corn silage (1:1) (mixed group, MG), and oat hay only (oat hay group, OHG). The nutrient digestion and metabolism of each group were measured, and the pH and rumen microflora were examined after feeding for different durations. Dynamic changes in microbial communities were detected. The nutrient digestion and metabolism results showed that, with an increase in the content of oat hay in the diet, the intake and apparent digestibility of dry matter (DM) and organic matter (OM) showed an increasing trend, and the intake, digestion, and stability of acid detergent fiber (ADF) and neutral detergent fiber (NDF) increased in the OHG. The apparent digestibility, dietary nitrogen, deposited nitrogen, and nitrogen retention rate in this group were significantly higher than those in the CSG (p < 0.05). The rumen pH and sequencing results showed that the rumen fluid pH of the CSG was significantly lower than that of the OHG at 1 and 5 h (p < 0.05). The main microbial in the rumen of the three groups of sheep were Bacteroides, Sclerotium, and Proteus. The dominant taxon in the CSG was Prevotella, followed by Vibrio syringae, and the dominant taxon in the MG and OHG was Prevotella, followed by Rikenellaceae. Redundancy analysis showed that ADF and NDF in the feed had an effect on the abundance of Fibrobacteres, Ruminococcaceae, and Prevotella. Our findings indicate that the use of oat hay roughage in the diet significantly improves the apparent digestibility of NDF and ADF and helps maintain the stable state of the sheep’s rumen internal environment and the growth of rumen microorganisms.

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

Commensal microorganisms present at mucosal surfaces play a vital role in protecting the host organism from bacterial infection. There are multiple factors that contribute to selecting for the microbiome, key of which are host genetics. Flavobacterium psychrophillum, the causative agent of Bacterial Cold Water Disease in salmonids, accounts for acute losses in wild and farmed Rainbow Trout (Oncorhynchus mykiss). The U.S. National Center for Cool and Cold Water Aquaculture has used family-based selective breeding to generate a line of rainbow trout with enhanced resistance to F. psychrophilum. The goal of this study is to determine whether selective breeding impacts the gut and gill microbiome of the F. psychrophilum-resistant as compared to a background matched susceptible trout line. Mid-gut and gill samples were collected from juvenile fish (mean bwt 118g) and microbial diversity assessed by 16S rDNA amplicon sequencing. Results indicate that alpha diversity was significantly higher in the mid-gut of the susceptible line compared to the resistant line, while no significant differences in alpha diversity were observed in the gills. Mycoplasma sp. was the dominant taxon in the mid-gut of both groups, although it was present at a decreased abundance in the susceptible line. We also observed an increased abundance of taxa that could potentially be pathogenic in the susceptible line, including Brevinema sp. and Enterobacteriaceae members. Within the gills, both lines exhibited similar microbial profiles, with Candidatus Branchiomonas being the dominant taxon. Together, these results suggest that selectively bred Flavobacterium psychrophillum-resistant trout may harness a more resilient gut microbiome, attributing to the disease resistant phenotype, providing a framework for future experiments.

Macrozoobenthic community structure of İğneada region in Turkey (the southwestern Black Sea)

The present study deals with macrozoobenthic species on soft substrates in İğneada (Turkish coast of the Black Sea). Benthic samples were collected seasonally at three stations between 2012 and 2013. A total of 155 species belonging to seven taxa (Turbellaria, Nemertea, Nematoda, Oligochaeta, Polychaeta, Crustacea, Phoronida, Mollusca, Hemichordata) were identified. Of these, four species are new records for the Black Sea fauna, 15 species are new to the Turkish coast of the Black Sea; and two species are new to the Turkish Seas. Polychaeta was the most representative taxon in the study area – it was represented by 58 species (39% of the total number of species). In terms of the number of individuals, Mollusca were the dominant taxon in all seasons (82% of the total number of individuals). The most dominant species were

The nocturnal bottleneck and the evolution of activity patterns in mammals

In 1942, Walls described the concept of a ‘nocturnal bottleneck’ in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.

Dynamics of the phytoplankton community in mesotrophic Lake Borówno

The phytoplankton in Lake Borówno has never been included in phycological studies. The objective of our research was qualitative and quantitative analysis with reference to physicochemical parameters. Qualitative and quantitative analysis of phytoplankton assemblages were performed in 2004 and 2009. A total of 117 taxa were identified in Lake Borówno: Cyanoprocaryota — 35, Cryptophyta — 2, Euglenophyta — 1, Pyrophyta — 3, Chrysophyceae — 4, Bacillariophyceae — 25, Chlorophyta — 47. The bottom of the shallow water was covered with meadows of Charophyceae, with the dominant species Chara vulgaris L.Biomass of the phytoplankton varied from 1.23 mg dm−3 in April to 5.74 mg dm−3 in August 2009. Ceratium hirundinella (O.F.Müller) Bergh was the dominant taxon during the whole season, but during summer another co-dominant taxon, Microcystis aeruginosa (Kütz.)Kütz., occurred.The quality parameters, phytoplankton biomass, chlorophyll-a concentration and TSI indicate the mesotrophic character of the lake. The blue-green algae blooms, which are the major problem for preserving the good conditions of water in lakes, were not observed either in 2004 or 2009.

Addition to the Late Cretaceous Laño mammal faunule (Spain) and to the knowledge of European “Zhelestidae” (Lainodontinae nov.)

New mammal material from the Campano-Maastrichtian locality of Laño, Spanish Basque Country documents two new zhelestid eutherian species referred to the genus Lainodon. This material enlightens the upper molar pattern of the European zhelestids and confirms their originality and homogeneity. The European zhelestids are included in the new subfamily Lainodontinae, which is distinct and characterized by a mosaic of primitive and specialized features. The Lainodontinae clade adds to other endemic vertebrate taxa (among multituberculates, flightless birds, dinosaurs, and turtles) that typify the Late Cretaceous fauna of the European Archipelago. The material from Laño provides further evidence of a modest but significant lainodontine radiation known by five or six species belonging to two or three genera (Lainodon, Labes, ? Valentinella), which is currently restricted to western Europe, i.e. to the Ibero-Armorican Island. The plesiomorph features of the Lainodontinae (lower molar trigonid poorly compressed, upper molar without lingual cingulum) recall the earliest known zhelestids, and suggest an Asian origin from a Sheikhdzheilia-like stem lineage at the beginning of the Late Cretaceous. This dispersal event from Asia probably involved other vertebrate taxa, such as the multituberculate stem group of the kogaionid mammals and the hadrosaurid dinosaurs. The zhelestid subfamily Lainodontinae represents the most diverse and dominant taxon in the western European Late Cretaceous mammal fauna, which is eutherian-dominated, by contrast to the eastern European Late Cretaceous mammal fauna which is dominated by an original and at that time exclusive radiation of kogaionid multituberculates.

Acartia tonsa production in the Patos Lagoon estuary, Brazil

Muxagata, E., Amaral, W. J. A., and Barbosa, C. N. 2012. Acartia tonsa production in the Patos Lagoon estuary, Brazil. – ICES Journal of Marine Science, 69: 475–482. Acartid copepods are abundant in estuaries, harbours, and semi-enclosed waters. A monitoring programme with the objective of evaluating copepod production, particularly that of Acartia tonsa, the dominant taxon in the Patos Lagoon estuary, was implemented. Zooplankton samples are collected monthly from two fixed locations with bongo nets 30 cm in diameter with nets of 90 and 200 μm mesh. Over a full year, 33 quantitative samples were analysed; copepods represented 40% of the organisms collected with the 90-μm mesh. Adults and copepodites of A. tonsa accounted for ∼19% of the total copepod fauna at both locations. Daily production rates of A. tonsa were calculated as 0.40 mg C m−3 d−1 for the inner estuary and 3.65 mg C m−3 d−1 in the channel. The value of 1 333 mg C m−3 year−1 calculated for A. tonsa at the channel station is very high relative to the situation in other estuaries, indicating that the estuary has a high production of copepods.