Efficacy of Utilization of All-Plant-Based and Commercial Low-Fishmeal Feeds in Two Divergently Selected Strains of Rainbow Trout (Oncorhynchus mykiss): Focus on Growth Performance, Whole-Body Proximate Composition, and Intestinal Microbiome

Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance

Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.

Impacts of alfalfa nutrient concentrate on pellet physical attributes, growth performance, metabolism and nutritional quality of rainbow trout, Oncorhynchus mykiss

This study addressed the escalating demand for aquatic feed by exploring the potential of alfalfa nutrient concentrate (ANC) as feed ingredient for rainbow trout. Test diets contained varying ANC levels (0%, 5%, 10%, 15%, and 20%) to replace fishmeal (32% in the 0% ANC diet) to achieve equal digestible protein and were processed using a cooking extrusion method. Analysis of feed pellets showed that pellet density increased with ANC levels (P < 0.001), resulting in sinking pellets at 20% ANC. Water stability and durability were improved while oil leakage decreased with increasing ANC levels (P < 0.05). Two feeding trials were conducted to test the diets in flow-through water systems with three replicates per diet. The first 10-week trial evaluated their impact on feeding, fecal physical quality, and the apparent digestibility coefficient (ADC) of dietary nutrients in rainbow trout (initial body weight 18.0 ± 0.2 g). ANC inclusion did not impact the palatability and satiety feed intake of the fish (P > 0.05). However, the ADC of dry matter and phosphorus significantly decreased in fish fed the 20% ANC diet (P < 0.05). The second 9-week trial investigated the growth performance, nutrition quality, and metabolism of rainbow trout (initial body weight 19.0 ± 0.2 g). While all fish exhibited substantial growth, fish fed diets with 10% to 20% ANC displayed lower specific growth rate and higher feed conversion ratio compared to those fed with 0% or 5% ANC (P < 0.05). The whole body protein content was higher in fish fed 5% ANC compared to all other treatments (P = 0.030). The biochemical parameters of plasma were similar across treatments, except for a decrease in plasma phosphorus levels in fish fed a 10% ANC diet compared to those fed a 0% ANC diet (P = 0.033). Significant changes were observed in liver metabolism including tricarboxylic acid cycle, amino acid and energy metabolism pathways in fish fed the 20% ANC diet versus the 0% ANC diet (P < 0.05). These results demonstrate that ANC inclusion improved pellet physical quality without impairing feeding behavior and nutritional quality of the fish but inclusion ≥10% in the diet reduced fish growth. This study offers the first comprehensive assessment of the potential of ANC used in fish feed involving feed management, feeding evaluation, and the biological response.

Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability

AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation. Here, we test some of the assumptions underlying the concept of hologenomic evolution using a unique experimental evolution model: lines of the bank vole (Myodes [=Clethrionomys] glareolus) selected for increased ability to cope with a low-quality herbivorous diet and unselected control lines. Results from a complex nature-nurture design, in which we combined cross-fostering between the selected and control lines with dietary treatment, showed that the herbivorous voles harbored a cecal microbiome with altered membership and structure and changed abundances of several phyla and genera regardless of the origin of their foster mothers. Although the differences were small, they were statistically significant and partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Thus, the results support the hypothesis that selection on a host performance trait leads to genetic changes in the host that promote the maintenance of a beneficial microbiome. Such a result is consistent with some of the assumptions underlying the concept of hologenomic evolution.

Effects of plant-based proteins and handling stress on intestinal mucus microbiota in rainbow trout

Via 16S rRNA gene amplicon sequencing, this study explores whether the gut mucus microbiota of rainbow trout is affected by the interaction of a plant-protein-based diet and a daily handling stressor (chasing with a fishing net) across two genetic lines (A, B). Initial body weights of fish from lines A and B were 124.7 g and 147.2 g, respectively. Fish were fed 1.5% of body weight per day for 59 days either of two experimental diets, differing in their fish meal [fishmeal-based diet (F): 35%, plant-based diet (V): 7%] and plant-based protein content (diet F: 47%, diet V: 73%). No diet- or stress-related effect on fish performance was observed at the end of the trial. However, we found significantly increased observed ASVs in the intestinal mucus of fish fed diet F compared to diet V. No significant differences in Shannon diversity could be observed between treatments. The autochthonous microbiota in fish fed with diet V was dominated by representatives of the genera Mycoplasma, Cetobacterium, and Ruminococcaceae, whereas Enterobacteriaceae and Photobacterium were significantly associated with diet F. The mucus bacteria in both genetic lines were significantly separated by diet, but neither by stress nor an interaction, as obtained via PERMANOVA. However, pairwise comparisons revealed that the diet effect was only significant in stressed fish. Therefore, our findings indicate that the mucus-associated microbiota is primarily modulated by the protein source, but this modulation is mediated by the stress status of the fish.

New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal

The formulation of sustainable fish feeds based on plant ingredients supplemented by alternative ingredients to plant (insect, micro-algae, yeast) and genetic selection of fish for plant-based diets were tested on rainbow trout in two separate experiments. Plant-based diets and corresponding diets supplemented with an ingredient mix: insect, micro-algae and yeast in Experiment A, and insect and yeast in Experiment B were compared to commercial-like diets. In experiment A, the mix-supplemented diet was successful in compensating the altered growth performance of fish fed their respective plant-based diet compared to those fed the commercial diet, by restoring feed conversion. In experiment B, the selected line demonstrated improved growth performances of fish fed mix-supplemented and plant-based diets compared to the non-selected line. Metabolomics demonstrated a plasma compositional stability in fish fed mix-supplemented and basal plant-based diets comprising an amino acid accumulation and a glucose depletion, compared to those fed commercial diets. The selected line fed mix-supplemented and commercial diets showed changes in inositol, ethanol and methanol compared to the non-selected line, suggesting an involvement of microbiota. Changes in plasma glycine-betaine content in fish fed the mix-supplemented diet suggest the ability of the selected line to adapt to alternative ingredients.

Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream (Sparus aurata) Production Cycle

Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5-7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t0; November 2019), intermediate (t1; July 2020) and final (t2; November 2020) sampling points were used for Illumina 16S rRNA gene amplicon sequencing of the adherent microbiota of anterior intestine (AI). Samples from the same individuals (t1) were also used for the gene expression profiling of AI by RNA-seq, and subsequent correlation analyses with microbiota abundances. Discriminant analyses indicated the gut bacterial succession along the production cycle with the proliferation of some valuable taxa for facing seasonality and different developmental stages. An effect of genetic background was evidenced along time, decreasing through the progression of the trial, namely the gut microbiota of GS fish was less influenced by changes in diet composition. At the same time, these fish showed wider transcriptomic landmarks in the AI to cope with these changes. Our results highlighted an enhanced intestinal sphingolipid and phospholipid metabolism, epithelial turnover and intestinal motility in GS fish, which would favour their improved performance despite the lack of association with changes in gut microbiota composition. Furthermore, in GS fish, correlation analyses supported the involvement of different taxa with the down-regulated expression of pro-inflammatory markers and the boosting of markers of extracellular remodelling and response to bacterium. Altogether, these findings support the combined action of the gut microbiome and host transcriptionally mediated effects to preserve and improve gut health and function in a scenario of different growth performance and potentiality.