Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing

Background Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota’s role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. Results Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. Conclusions This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.

Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)

Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individuals sampled during both active and hibernation seasons. The existing reference annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals was mapped to the new reference annotation to quantify differential isoform usage between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of differential isoform usage with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that differential isoform usage, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.

Influence of conditions of keeping bee families in wintering on their productivity

Creating favorable conditions for the development of bee colonies, adherence to technological techniques and processes are of great importance in increasing productivity. The article highlights the results of research on the impact of increased subframe space during the wintering of bee colonies on their further development and productivity. In the course of the research, bee colonies were evaluated on the basis of a set of economically useful traits. For research, 2 groups of bee colonies were identified, 10 in each, equivalent in strength and food security, with young fertile queens bred in the same year. The formation of experimental groups took into account the strength of bee colonies, the number of closed brood, the age of the queens, the availability of feed (honey and perga), and the quality of nest cells. These indicators in the experimental groups were almost the same. When preparing bee colonies for winter, the frames in the families of the control group were in the center of the hive, removed the top insulation and unscrewed the sheets by 5–7 sm in the experimental group performed the same actions as in the control winters substituted empty store extensions, thus increasing the subframe space. During the research, honey and wax productivity, strength of families in different periods of the active season and winter hardiness were determined. It was found that bees kept in the hives with increased subframe space, in which 76.1 % less plague was detected, compared with the control group, tolerate wintering well. These families are developing more intensively in the spring and summer period – the advantage in strength was 25.8 % in April, 31.4 % in May, and 31.6 % in June. And further they show higher honey and wax productivity by 24.9 and 32.1 %, respectively.

Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees

There is increasing evidence that honeybees (Apis mellifera L.) can adapt naturally to survive Varroa destructor, the primary cause of colony mortality world-wide. Most of the adaptive traits of naturally varroa-surviving honeybees concern varroa reproduction. Here we investigate whether factors in the honeybee metagenome also contribute to this survival. The quantitative and qualitative composition of the bacterial and viral metagenome fluctuated greatly during the active season, but with little overall difference between varroa-surviving and varroa-susceptible colonies. The main exceptions were Bartonella apis and sacbrood virus, particularly during early spring and autumn. Bombella apis was also strongly associated with early and late season, though equally for all colonies. All three affect colony protein management and metabolism. Lake Sinai virus was more abundant in varroa-surviving colonies during the summer. Lake Sinai virus and deformed wing virus also showed a tendency towards seasonal genetic change, but without any distinction between varroa-surviving and varroa-susceptible colonies. Whether the changes in these taxa contribute to survival or reflect demographic differences between the colonies (or both) remains unclear.

The influence of night length: Activity of the northern bat Eptesicus nilssonii under conditions of continuous light in midnight sun compared to a southern population

Background Nearly all insectivorous bats (Chiroptera) are strictly nocturnal, flying and feeding only between sunset and sunrise despite lower insect availability than by day, most likely to avoid predation by diurnal birds. This may represent a great challenge to bats living north of the Arctic Circle, which are exposed to bright nights in the period of the midnight sun. The northern bat Eptesicus nilssonii was studied at different latitudes in Norway (69, 66 and 58°N) by three techniques; visual counts of exits from and returns to roosts, infrared detection with a datalogger and an ultrasound data recorder, to reveal how their activity varied across latitude, season, and night, as well as across light levels. How does a nocturnal bat adjust to perpetual light and what light levels are tolerated? Results In the north the bats’ active season lasted 2.5 months, 1.5 months shorter than in the south. The bats only flew in 3-4 weeks of midnight sun, and hardly ever left the roost until the sun went behind a hill in the evening. In addition, the timing of their nightly hunting was highly influenced by the darkness of the sky, and they very rarely flew in light levels above 200 foot-candles (FC). As the night became darker than twilight from early August, the bats restricted their activity to between sunset and sunrise. This was the normal situation in southern Norway, where the bats tracked sunset and sunrise throughout the entire season. Those bats appeared to prefer light levels below 100-50 FC and hence, also did fly in twilight conditions. Conclusions The willingness to fly in twilight by the southern population may be a prerequisite to the northern bat’s survival in the land of the midnight sun. These bats must accept short nights in the first part of their summer season and must be willing to fly in light levels 2-4 times higher than in the south. Most likely, this depends on a reduced predation risk and good abundance of insects at night.

Firmicutes and Bacteroidetes explain mass gain variation in an obligate hibernator

Body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well documented that symbiotic microorganisms play a vital role in animal physiology and behaviour. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity; Firmicutes is consistently associated with obesity while Bacteroidetes is associated with leanness both in humans and other animals.The focus of most microbiome studies has been on human health or involved lab reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we test whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes are associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by quantifying microbial abundance over five years of fecal samples (2015 - 2019) collected during their summer active season. Results show that marmots with higher mass gain rates have a greater abundance of Firmicutes. In contrast, higher abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates, and similarly in harsher environments. Although correlative, these results highlight the importance of symbiotic gut microbiota to mass gain in the wild, a trait associated with survival and fitness in many taxonomic groups.

Food consumption and winter mortality in bee colonies wintering in hives made from different materials with lattice and solid bottom

The objective of the present study is to examine the changes in some indicators characterizing the winter hardiness of bee colonies settled in hives made of different material (polystyrene, wood, ceramics) and with different type of bottom (lattice or solid). Some parameters which characterize the wintering of bee colonies (amount of dead bees and quantity of food consumption in winter) have been investigated. The bee colonies were housed in 10-frame Dadant Blatt hives with a lattice and solid bottom situated at the Training Apiary of the Faculty of Agriculture, Trakia University, Stara Zagora, Bulgaria. Two inspections of the bee colonies were carried out (during wintering in November 2020 and at the beginning of the active season in March 2021). Amount of bees in the bee hive (strength) and amount of capped honey in the honeycombs were reported. In bee colonies wintering in hives with a lattice bottom, the consumption of food per 1 kg of bees was 1.639 kg (50%) higher than in hives with a solid bottom. Winter mortality of bees in hives with a lattice bottom was higher compared to this indicator in the hives with a solid bottom, 16.19±10.72% and 12.59±3.57%, respectively, which can be considered excellent wintering below 15% and good wintering in the range of 15.0-19.99%.

Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing

Background Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota’s role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to sequence the microbiotas of an obligate rodent hibernator, we also reported changes in captive TLGS microbiotas across the year (summer, winter, and spring). Results Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. Conclusions This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to investigate the microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported seasonal changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.