Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish
The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
Nyholm et al. (2022) Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish. PeerJ 10:e12992 https://doi.org/10.7717/peerj.12992
Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)
Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.
Lan et al. (2022) Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PeerJ 10:e12993 https://doi.org/10.7717/peerj.12993
Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow
Objective The purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow. Methods To determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight. Results Soluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments. Conclusion A diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation.
Choi et al. (2022) Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow. PeerJ 10:e12998 https://doi.org/10.7717/peerj.12998
Functional network motifs defined through integration of protein-protein and genetic interactions
Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
Sahoo et al. (2022) Functional network motifs defined through integration of protein-protein and genetic interactions. PeerJ 10:e13016 https://doi.org/10.7717/peerj.13016
Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat
Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.
Yasin et al. (2022) Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat. PeerJ 10:e12808 https://doi.org/10.7717/peerj.12808
Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1
Inorganic and synthetic flocculants are widely investigated for removing harmful microalgae, such as Microcystis aeruginosa. However, their toxicity and non-biodegradability are shortcomings. Bioflocculants based on extracellular polysaccharides have attracted much attention as alternative flocculants. However, its high production cost is a limiting factor for applying bioflocculants. Here, we investigate the potential of the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1, as a novel flocculant on M. aeruginosa cells. The removal efficiency of M. aeruginosa cells by the dead cells was measured by mixing and shaking both components in a buffer with 5 mM CaCl2 in different incubation times and concentrations of the dead cells. After that, the minimum effective concentration of CaCl2 was determined. The combination effect of FeCl3 and the dead cells on the removal efficiency was tested. The structure of cell aggregates consisted of the dead cells and M. aeruginosa cells were also observed using a scanning electron microscope. The maximum removal efficiency (75.39%) was reached within 3 min in the presence of CaCl2 when 5 mg/ml of the dead cells (wet cells) were added. The optimal concentration of CaCl2 was 5 mM. The combination of the dead cells and a low concentration of FeCl3 (10 mg/L) with 5 mM of CaCl2 significantly improved the removal efficiency by about 1.2 times (P < 0.05). This result indicates that the combination usage of the dead cells can reduce the use of FeCl3. These results indicated that the dead cells could potentially be a novel biolfocculant to remove M. aeruginosa cells.
Environmental Contamination and Remediation
Furusawa et al. (2022) Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1. PeerJ 10:e12867 https://doi.org/10.7717/peerj.12867
Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.)
Laccase, as a copper-containing polyphenol oxidase, primarily functions in the process of lignin, anthocyanin biosynthesis, and various abiotic/biotic stresses. In this study, forty-eight laccase members were identified in the eggplant genome. Only forty-two laccase genes from eggplant (SmLACs) were anchored unevenly in 12 chromosomes, the other six SmLACs were mapped on unanchored scaffolds. Phylogenetic analysis indicated that only twenty-five SmLACs were divided into six different groups on the basis of groups reported in Arabidopsis. Gene structure analysis revealed that the number of exons ranged from one to 13. Motif analysis revealed that SmLACs included six conserved motifs. In aspects of gene duplication analysis, twenty-one SmLACs were collinear with LAC genes from Arabidopsis, tomato or rice. Cis-regulatory elements analysis indicated many SmLACs may be involved in eggplant morphogenesis, flavonoid biosynthesis, diverse stresses and growth/development processes. Expression analysis further confirmed that a few SmLACs may function in vegetative and reproductive organs at different developmental stages and also in response to one or multiple stresses. This study would help to further understand and enrich the physiological function of the SmLAC gene family in eggplant, and may provide high-quality genetic resources for eggplant genetics and breeding.
Wan et al. (2022) Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.). PeerJ 10:e12922 https://doi.org/10.7717/peerj.12922
Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations
Background Fuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated. Methods This study used next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China. Results The results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.
Miao et al. (2022) Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations. PeerJ 10:e12927 https://doi.org/10.7717/peerj.12927
Drivers of phenotypic divergence in a Mesoamerican highland bird
Animals derive their coloration from a variety of pigments as well as non-pigmentary structural features. One of the most widespread types of pigments are carotenoids, which are used by all invertebrate taxa and most vertebrate orders to generate red, pink, orange and yellow coloration. Despite their widespread use by diverse animal groups, animals obligately obtain carotenoid pigments from diet. Carotenoid-based coloration is therefore modulated by evolutionary and ecological processes that affect the acquisition and deposition of these pigments into tegumentary structures. The Flame-colored Tanager (Piranga bidentata) is a highland songbird in the cardinal family (Cardinalidae) that is distributed from Mexican sierras through Central America up to western Panama. While female plumage throughout its entire range is predominantly yellow, males exhibit a noticeable split in ventral plumage color, which is bright orange on the West slope and the Tres Marias Islands and blood red in Eastern Mexico and Central America. We used Multiple Regression on Matrices (MRM) to evaluate the relative contributions of geographic distance, climate and genetic distance on color divergence and body differences between geographically disjunct populations. We found that differentiation in carotenoid plumage coloration was mainly explained by rainfall differences between disjunct populations, whereas body size differences was best explained by variation in the annual mean temperature and temperature of coldest quarter. These results indicate that climate is a strong driver of phenotypic divergence in Piranga bidentata.
Robles-Bello et al. (2022) Drivers of phenotypic divergence in a Mesoamerican highland bird. PeerJ 10:e12901 https://doi.org/10.7717/peerj.12901
Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast
Background Many migrant birds have been returning to Europe earlier in spring since the 1980s. This has been attributed mostly to an earlier onset of spring in Europe, but we found the timing of Willow Warblers’ passage to be influenced by climate indices for Africa as much as those for Europe. Willow Warblers’ spring passage through northern Europe involves populations from different wintering quarters in Africa. We therefore expected that migration timing in the early, middle and late periods of spring would be influenced sequentially by climate indices operating in different parts of the winter range. Methods Using data from daily mistnetting in 1 April–15 May over 1982–2017 at Bukowo (Poland, Baltic Sea coast), we derived an Annual Anomaly (AA, in days) of Willow Warbler spring migration. We decomposed this anomaly into three main periods (1–26 April, 27 April–5 May, 6–15 May); one-third of migrants in each period. We modelled three sequential time series of spring passage using calendar year and 15 large-scale climate indices averaged over the months of Willow Warblers’ life stages in the year preceding spring migration as explanatory variables in multiple regression models. Nine climate variables were selected in the best models. We used these nine explanatory variables and calculated their partial correlations in models for nine overlapping sub-periods of AA. The pattern of relationships between AA in these nine sub-periods of spring and the nine climate variables indicated how spring passage had responded to the climate. We recommend this method for the study of birds’ phenological responses to climate change. Results The Southern Oscillation Index and Indian Ocean Dipole in Aug–Oct showed large partial correlations early in the passage, then faded in importance. For the Sahel Precipitation Index (PSAH) and Sahel Temperature Anomaly (TSAH) in Aug–Oct partial correlations occurred early then peaked in mid-passage; for PSAH (Nov–March) correlations peaked at the end of passage. NAO and local temperatures (April–May) showed low correlations till late April, which then increased. For the Scandinavian Index (Jun–Jul) partial correlations peaked in mid-passage. Year was not selected in any of the best models, indicating that the climate variables alone accounted for Willow Warblers’ multiyear trend towards an earlier spring passage. Discussion Climate indices for southern and eastern Africa dominated relationships in early spring, but western African indices dominated in mid- and late spring. We thus concluded that Willow Warblers wintering in southern and eastern Africa dominated early arrivals, but those from western Africa dominated later. We suggest that drivers of phenological shifts in avian migration are related to changes in climate at remote wintering grounds and at stopovers, operating with climate change in the north, especially for species with complex and long-distance migration patterns.
Remisiewicz et al. (2022) Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast. PeerJ 10:e12964 https://doi.org/10.7717/peerj.12964