Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus). Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1). Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation

A Proposed Taxonomy of Anaerobic Fungi (Class Neocallimastigomycetes) Suitable for Large-Scale Sequence-Based Community Structure Analysis

Anaerobic fungi are key players in the breakdown of fibrous plant material in the rumen, but not much is known about the composition and stability of fungal communities in ruminants. We analyzed anaerobic fungi in 53 rumen samples from farmed sheep (4 different flocks), cattle, and deer feeding on a variety of diets. Denaturing gradient gel electrophoresis fingerprinting of the internal transcribed spacer 1 (ITS1) region of the rrn operon revealed a high diversity of anaerobic fungal phylotypes across all samples. Clone libraries of the ITS1 region were constructed from DNA from 11 rumen samples that had distinctly different fungal communities. A total of 417 new sequences were generated to expand the number and diversity of ITS1 sequences available. Major phylogenetic groups of anaerobic fungi in New Zealand ruminants belonged to the genera Piromyces, Neocallimastix, Caecomyces and Orpinomyces. In addition, sequences forming four novel clades were obtained, which may represent so far undetected genera or species of anaerobic fungi. We propose a revised phylogeny and pragmatic taxonomy for anaerobic fungi, which was tested and proved suitable for analysis of datasets stemming from high-throughput next-generation sequencing methods. Comparing our revised taxonomy to the taxonomic assignment of sequences deposited in the GenBank database, we believe that >29% of ITS1 sequences derived from anaerobic fungal isolates or clones are misnamed at the genus level

Replicate and randomize, or lie

Biological populations are naturally variable. Investigators need to replicate observations to estimate their characteristics. They must also randomize selection to estimate those characteristics without bias and with known confidence. Both replication and randomization are necessary

Reindeer in the Arctic reduce sleep need during rumination.

Timing and quantity of sleep depend on a circadian (∼24-h) rhythm and a specific sleep requirement. <sup>1</sup> Sleep curtailment results in a homeostatic rebound of more and deeper sleep, the latter reflected in increased electroencephalographic (EEG) slow-wave activity (SWA) during non-rapid eye movement (NREM) sleep. <sup>2</sup> Circadian rhythms are synchronized by the light-dark cycle but persist under constant conditions. <sup>3</sup> <sup>,</sup> <sup>4</sup> <sup>,</sup> <sup>5</sup> Strikingly, arctic reindeer behavior is arrhythmic during the solstices. <sup>6</sup> Moreover, the Arctic's extreme seasonal environmental changes cause large variations in overall activity and food intake. <sup>7</sup> We hypothesized that the maintenance of optimal functioning under these extremely fluctuating conditions would require adaptations not only in daily activity patterns but also in the homeostatic regulation of sleep. We studied sleep using non-invasive EEG in four Eurasian tundra reindeer (Rangifer tarandus tarandus) in Tromsø, Norway (69°N) during the fall equinox and both solstices. As expected, sleep-wake rhythms paralleled daily activity distribution, and sleep deprivation resulted in a homeostatic rebound in all seasons. Yet, these sleep rebounds were smaller in summer and fall than in winter. Surprisingly, SWA decreased not only during NREM sleep but also during rumination. Quantitative modeling revealed that sleep pressure decayed at similar rates during the two behavioral states. Finally, reindeer spent less time in NREM sleep the more they ruminated. These results suggest that they can sleep during rumination. The ability to reduce sleep need during rumination-undisturbed phases for both sleep recovery and digestion-might allow for near-constant feeding in the arctic summer

Digestive challenges for vertebrate animals: Microbial diversity, cardiorespiratory coupling, and dietary specialization

Also published as: Molecules to Migration: Pressures of Life: the Fourth International Conference in Africa for Comparative Physiology and Biochemistry, Maasai Mara National Reserve, Kenya, 2008, 2010; pp.764-774The digestive system is the interface between the supply of food for an animal and the demand for energy and nutrients to maintain the body, to grow, and to reproduce. Digestive systems are not morphologically static but rather dynamically respond to changes in the physical and chemical characteristics of the diet and the level of food intake. In this article, we discuss three themes that affect the ability of an animal to alter digestive function in relation to novel substrates and changing food supply: (1) the fermentative digestion in herbivores, (2) the integration of cardiopulmonary and digestive functions, and (3) the evolution of dietary specialization. Herbivores consume, digest, and detoxify complex diets by using a wide variety of enzymes expressed by bacteria, predominantly in the phyla Firmicutes and Bacteroidetes. Carnivores, such as snakes that feed intermittently, sometimes process very large meals that require compensatory adjustments in blood flow, acid secretion, and regulation of acid‐base homeostasis. Snakes and birds that specialize in simple diets of prey or nectar retain their ability to digest a wider selection of prey. The digestive system continues to be of interest to comparative physiologists because of its plasticity, both phenotypic and evolutionary, and because of its widespread integration with other physiological systems, including thermoregulation, circulation, ventilation, homeostasis, immunity, and reproduction.P. S. Barboza, A. Bennett, J.-H. Lignot, R. I. Mackie, T. J. McWhorter, S. M. Secor, N. Skovgaard, M. A. Sundset, T. Wan