Functional-trait ecology of the plateau pika Ochotona curzoniae in the Qinghai-Tibetan Plateau ecosystem

Understanding a species' functional traits allows for a directed and productive perspective on the role a species plays in nature, and thus its relative importance to conservation planning. The functional-trait ecology of the plateau pika Ochotona curzoniae is examined to better understand the resilience and sustainability of the high alpine grasslands of the Qinghai-Tibetan Plateau (QTP). The key functional traits of plateau pikas are their abundance and behavior of digging extensive burrow systems. Plateau pikas have been poisoned over a significant part of their original geographic distribution across the QTP, allowing comparison of ecological communities with and without pikas. Nearly all mammalian and avian carnivores, most of which are obligate predators on pikas, have been lost in regions where pikas have been poisoned. Most endemic birds on the QTP nest in pika burrows; when pikas are poisoned, burrows collapse, and these birds are greatly reduced in number. Due to the biopedturbation resulting from their burrows, regional plant species richness is higher in areas with pikas than without. The presence of pika burrows allows higher rates of infiltration during heavy monsoon rains compared to poisoned areas, possibly mitigating runoff and the potential for serious downslope erosion and flooding. Thus, the functional traits of plateau pikas enhance native biodiversity and other important ecosystem functions; these traits are irreplaceable. As plateau pikas are not natural colonizers, active re-introduction programs are needed to restore pikas to areas from which they have been poisoned to restore the important functional ecological traits of pikas.

Gut microbiome adaptation to extreme cold winter in wild plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau is a harsh environment characterized by low temperature, high altitude and hypoxia, although some native mammals may adapt well to the extreme climate. However, how animal gut microbial community structure and function adapt to extreme cold climates is not well understood. Plateau pika (Ochotona curzoniae) is an ideal animal model with which to study the effects of climate change on host adaptation by studing intestinal microorganisms. Here, we used 16S rRNA sequencing technology combined with physiological methods to investigate plateau pika gut microbiota in summer and winter. Due to limited diet resources, the pikas in winter have a lower ability of degradation and fermentation for plant-based food (reduced cellulase activity and total short-chain fatty acids) by decreasing gut microbial diversity and some functional microbes, such as fiber-degrading bacteria Oscillospira and Treponema. Metagenomic prediction showed that most of those gene functions associated with metabolism (e.g. energy metabolism and lipid metabolism) were less abundant in winter, implying that the plateau pika slows diet fermentation and weakens energy requirements in the cold season. Our results have significance for explaining the mechanism of wild plateau mammals adapting to a high-altitude cold environment from the perspective of gut microbiome.

Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China

Four novel bacterial strains (ST-M6^T, L-033, L-031^T and Z-333) were isolated from the intestinal contents of plateau pikas (Ochotona curzoniae) collected on the Qinghai-Tibet Plateau, PR China. Cells were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, capsuled and short-rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequences and 387 core genes indicated that the four isolates belong in the genus Microbacterium and clearly separate from recognized species. The two type strains (ST-M6^T and L-031^T) shared low 16S rRNA similarity, average nucleotide identity values and digital DNA-DNA hybridization relatedness with their phylogenetic neighbours (Microbacterium ginsengisoli DSM 18659^T, Microbacterium hatanonis DSM 19179^T, Microbacterium rhizomatis JCM 30598^T, Microbacterium radiodurans CCTCC M208212^T, Microbacterium oleivorans DSM 16091^T and Microbacterium arborescens DSM 20754^T). The genomic DNA G+C contents of strains ST-M6^T and L-031^T were 70.4 and 70.7 mol%, respectively. The major cellular fatty acids of strain ST-M6^T were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0, in contrast to anteiso-C_17 : 0, anteiso-C_15 : 0 and anteiso-C_17 : 1  ω9c of strain L-031^T. Both type strains (ST-M6^T and L-031^T) were glycolate test positive and shared the following common features: MK-11 and MK-12 as major menaquinones; rhamnose, ribose, mannose and galactose as major cell-wall sugars; diphosphatidylglycerol, phosphatidylglycerol and two glycolipids as polar lipids; and ornithine, alanine, glycine and glutamic acid as cell-wall amino acids. Comparing the phenotypic, phylogenetic and chemotaxonomic features of the four strains and their related taxa, strains ST-M6^T and L-031^T represent two novel species of the genus Microbacterium, for which the names Microbacterium caowuchunii sp. nov. (type strain ST-M6^T=CGMCC 1.16364^T=DSM 104058^T) and Microbacterium lushaniae sp. nov. (type strain L-031^T =CGMCC 1.16363^T=DSM 106170^T) are proposed.

Effects of Plateau Pika Disturbance on the Spatial Heterogeneity of Vegetation in Alpine Meadows

Herbivory is one of the important factors that influence spatial heterogeneity of vegetation in grasslands. In this study, we focused on plateau pika (Ochotona curzoniae) to investigate the effects of the presence of small semi-fossorial herbivores and their disturbance intensity on the spatial heterogeneity of vegetation in alpine meadows across three sites in the Qinghai-Tibetan Plateau. A random stratified paired sampling method was used to collect vegetation data, and plant species richness at both fine and coarse scales were used to estimate the spatial heterogeneity of vegetation. This study showed that the presence of plateau pikas led to higher spatial heterogeneity of vegetation in alpine meadows, which increased linearly as the disturbance intensities of plateau pikas increased. The findings of this study demonstrate that small semi-fossorial herbivores have an important impact on the spatial heterogeneity of vegetation, and present a possible approach for estimating the effect of the presence of a small semi-fossorial herbivore and its disturbance intensity on the spatial heterogeneity of vegetation in grasslands.

Life-history traits and fitness of plateau pika (Ochotona curzoniae) in alpine meadow ecosystem

Plateau pika (Ochotona curzoniae) is an endemic mammal living in the alpine meadow ecosystem in Qinghai-Tibet Plateau. We studied life history of plateau pika by mark-recapturing method. The research results showed that fitness of plateau pika to its habitat was lower than those of many other mammal species; plateau pika adopted quick growth strategy; the life-history features of plateau pika were accorded with Charnov (Evolutionary Ecology Research, 2002, 4, 749)'s formula about life-history classification, that is, E/α ≈ 1.35, C·E ≈ 1.7, I/m ≈ 0.3, in which E stands for average adult life span; α stands for age at first reproduction; C is reproductive effort; I is the size of an offspring at independence from the parent; m is average adult body mass. There does not exist dimorphism in plateau pikas. The configurations of females and males are similar; the average body mass of males is a little heavier than that of females, but the difference is not significant (F = 1.0854, df = 154, p > .3058). The juveniles exhibit a J-form growth curve before 30-day age and grow slower between 30 and 65-day age and reach body mass equilibrium at about 65 days old. So, 65 days is the maturity age of plateau pika. There are 3 mortality peaks in plateau pika population. The first time is in neonate period, when only one half of juveniles can pass through this period, which implies that juvenile period is influenced strongly by natural selection; the second time is in fecundity peak period, which reflects the cost of reproduction; the third time is in the old age of plateau pika, a significant loss occurs during this period, which is the result of natural selection. The average longevity of females is longer than that of males. A female reaches the maximum life span recorded, that is, 931 days. The average longevity of all individuals is 16.33 months ≈ 490 days. The survival rate of females is higher than that of males, which reflects the cost of reproduction and society role of males. It is the outcome of natural selection. The sex ratio of neonates is 1:1; however, the sex ratio of adults is female: male = 1.31:1, which is caused by higher mortality of males over females in life history. Plateau pikas reproduced two times every year. The average gestation period of females is 18-20 days. The average litter size is 4.57 individual. The average body mass of neonates is 9.28 g. The average litter size of adult female plateau pika does not variate with age. Breeding season is between April and June. The reproductive value and fertility of 15-18 months age females are highest. The reproductive value and fertility increased with age before reproductive value and fertility peak age; however, the reproductive value and fertility decreased with age after peak age. The fitness of plateau pika (r = .1125) was lower than that of American pikas (O. princeps) (r = 2.172). The survival rate was the main factor influencing fitness. The dynamic trend of plateau pika population was coincident with r, that is, the plateau pika population was stable.

Plateau Pika Disturbance Changes Soil Bacterial Functions and Exoenzyme Abundance to Modulate the C Cycle Pathway in Alpine Grasslands

Plateau pika (Ochotona curzoniae) is crucial to soil organic carbon (SOC) storage in the Qinghai-Tibetan plateau (QTP), but its role in bacterial SOC metabolisms across different degraded alpine grasslands remains unclear. In this study, we investigated the soil physicochemical properties and the composition and function of the bacterial communities in control and pika-disturbed grasslands experiencing different degradation levels (undegraded, UDM; lightly, LDM; moderately, MDM and severely, SDM). The results demonstrate that (i) the primary bacterial phyla include Proteobacteria, Acidobacteriota, Actinobacteriota, Bacteroidota and Verrucomicrobiota. Soil physicochemical properties significantly impact the composition of the bacterial communities and determine the influence of pika disturbance. Pika disturbance increases bacterial OTUs by 7.5% in LDP (p > 0.05) and by 50.5% in MDP (p < 0.05), while decreases OTUs by 21.4% in SDP (p < 0.05). (ii) Pika disturbance downregulates the exoenzyme abundance associated with simple and complex organic matter decomposition by 9.5% and 13.9% in LDP, and 29.4% and 26.3% in MDP (p < 0.05), while upregulates these exoenzymes by 23.6% and 37.9% in SDP (p < 0.05). These changes correspond to the increase in TC and SOC in LDP and MDP but declines in SDP. (iii) Plateau pika disturbance can enhance SOC accumulation through upregulating the C cycle pathway of ethanol production in LDP and MDP. However, it upregulates the pathway of pyruvate to CO2 conversion in SDP, leading to negative influence on SOC storage.

Preference for ground cover when selecting burrow entrances in plateau pikas

Burrow-dwelling animals such as the plateau pika (Ochotona curzoniae) often seek sturdy entrances for their burrows, which can reduce the need for frequent maintenance. The toughness of the ground surface is often reinforced by the interweaving of plant roots and often varies with the root characteristics. To better understand ground cover preferences when selecting burrow entrances by plateau pikas, we investigated the ratios of different ground covers at the rear of the entrances, as well as their coverage and underlying soil compaction in an undegraded alpine meadow on the Qinghai-Xizang Plateau. The results indicated a clear preference hierarchy of sedges > forbs > grass > bare soil. This distribution was aligned with the soil compaction hierarchy of the topsoil layer beneath each cover type. The sedge coverage was significantly negatively correlated with burrow density, suggesting that plateau pikas opt for sturdy entrances with a natural inclination toward energy conservation. However, there is consensus that the population density of plateau pikas often reaches its maximum on almost nonvegetated "black soil beaches." We hypothesized that the survival benefits brought about by vegetation degradation would be higher than the maintenance costs of burrow entrances.

Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika

Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.

A non-destructive method for three-dimensional characterizing plateau pika's burrow system

The plateau pika's burrow system exerts a significant influence on the alpine ecosystem. However, current methods are insufficient for accurately characterizing its spatial structure. In this study, we utilized drone imagery and ground-penetrating radar (GPR) scanning in alpine grasslands on the eastern edge of the Qinghai-Tibetan Plateau (QTP). We developed a novel signal processing workflow for trajectory detection and reconstruction of the three-dimensional structure of pika's burrow systems. The results indicate that, within a 10 × 10 m study area, eight burrows were identified in moderately degraded grassland, including six simple burrows and two complex burrows. The longest tunnel measured 830 cm, with an average depth and diameter of 23.2 cm and 7.0 cm, respectively. These burrows accounted for 2.5% of the pika affected soil volume. In severely degraded grassland, twelve burrows were identified, with the longest tunnel measuring 580 cm, and an average depth and diameter of 15.6 cm and 7.0 cm, accounting for 5.2% of the pika affected soil volume. Compared to the extraction method, the values for length, depth, and orientation were largely consistent, although the diameter of burrows was slightly lower in GPR data. Regression analysis further confirmed the feasibility of proposed method. This non-destructive detection method provides critical technical support for studying the ecological impacts of burrow systems of fossorial animals on the QTP.

Nocardioides ochotonae sp. nov., Nocardioides campestrisoli sp. nov. and Nocardioides pantholopis sp. nov., isolated from the Qinghai-Tibet Plateau

Six Gram-stain-positive, aerobic and irregular-rod-shaped actinobacteria (ZJ1313^T, ZJ1307, MC1495^T, Y192, 603^T and X2025) were isolated from the Qinghai-Tibet Plateau of China and were characterized using a polyphasic taxonomic method. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the six new strains formed three distinct clusters within the genus Nocardioides, and strains ZJ1313^T and ZJ1307 were most closely related to N. solisilvae JCM 31492^T (16S rRNA gene sequence similarity, 98.0 %), MC1495^T and Y192 to N. houyundeii 78^T (98.5 %), and 603^T and X2025 to N. dokdonensis JCM 14815^T (97.6 %). The digital DNA-DNA hybridization values of strains ZJ1313^T, MC1495^T and 603^T among each other and with type strains of their closest relatives were all below the 70 % cut-off point, but values within each pair of new strains were all higher than the threshold. The major fatty acids of these strains were iso-C_16 : 0, C_17 : 1  ω8c or C_18 : 1  ω9c. MK-8(H₄) was the predominant respiratory menaquinone and ʟʟ-2,6-diaminopimelic acid was the diagnostic diamino acid. All the strains shared diphosphatidylglycerol (predominant), phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the common polar lipids, with minor difference in the types of unidentified phospholipids, glycolipids and lipids. The G+C contents based on genomic DNA of strains ZJ1313^T, MC1495^T and 603^T were 72.5, 72.1 and 73.2 mol%, respectively. The above results suggested that strain pairs ZJ1313^T/ZJ1307, MC1495^T/Y192 and 603^T/X2025 represent three new species of genus Nocardioides, for which the names Nocardioides ochotonae sp. nov. (ZJ1313^T=GDMCC 4.177^T=KCTC 49537^T=JCM 34185^T), Nocardioides campestrisoli sp. nov. (MC1495^T=GDMCC 4.176^T=KCTC 49536^T=JCM 34307^T) and Nocardioides pantholopis sp. nov. (603^T=CGMCC 4.7510^T=DSM 106494^T) are proposed accordingly.

Inhibitor screening of lactate dehydrogenase C4 from black-lipped pika in the Western Sichuan Plateau

Studies indicated that lactate dehydrogenase C4 (LDH-C4) was a good target protein for development of contraceptive drugs. Virtual screening and in vitro enzyme assay using pika LDH-C4 as target protein revealed NSC61610, NSC215718, and NSC345647 with Ki of 7.8, 27, and 41 μM separately. This study might be helpful for development of pika contraceptive drugs.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.