Fecal microbiota reveal adaptation of herbivores to the extreme environment of the Qinghai–Tibet Plateau

Background:Gut microbiota is pivotal in regulating hosts'biological processes and maintaining homeostasis,but knowledge about its role in wild herbivores in extreme environments remains limited.Methods:Gut bacteria and fungi were sequenced in ruminant(Chiru and Yak)and nonruminant(Kiang)herbivores on the Qinghai–Tibet Plateau,and their community structure,co-occurrence networks,functions,and assembly mechanisms were investigated using multivariate ecological and statistical methods.Results:Kiang had lower gut microbial diversity than Chiru and Yak.Bacterial host-specific exclusivity was greater than that of fungi.In addition to the evidence of glycan biosynthesis and carbohydrate metabolism,Chiru had a high Firmicutes/Bacteroidetes ratio and low animal pathogen abundance,suggesting better adaptation to the plateau's harsh environment.Additionally,members of gut microbiota tended to co-occur rather than co-exclude in all herbivores.Different network complexity and stability patterns were observed between bacterial and fungal communities.Furthermore,gut bacterial assembly was primarily controlled by stochastic dispersal limitation and drift,whereas fungal assembly was primarily controlled by deterministic homogeneous selection except in Chiru.Conclusions:On the Qinghai–Tibet Plateau,Chiru and Yak exhibit more diverse gut microbiota and more diverse metabolic functions than Kiang,and gut bacteria are more divergent than gut fungi in these herbivores.

Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences.However,the response mechanisms and pathways of the functional genes associated with the carbon(C)and nitrogen(N)cycling to cadaveric substances such as cadaverine and putrescine remain unclear.This study explored the variation of functional genes associated with C fixation,C degradation and N cycling and their influencing factors under cadaverine,putrescine and mixed treatments.Our results showed only putrescine significantly increased the alpha diversity of C fixation genes,while reducing the alpha diversity of N cycling genes in sediment.For the C cycling,the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes(i.e.,acsB and acsE)and lig gene linked to lignin degradation in water,while only significantly increasing the hydroxypropionate-hydroxybutylate cycle(i.e.,accA)gene abundance in sediment.For the N cycling,mixed treatment significantly decreased the abundance of the nitrification(i.e.,amoB),denitrification(i.e.,nirS3)genes in water and the assimilation pathway gene(i.e.,gdhA)in sediment.Environmental factors(i.e.,total carbon and total nitrogen)were all negatively associated with the genes of C and N cycling.Therefore,cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling,while promoting C degradation.These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

Gravesoil fungi are more sensitive than bacteria in response to precipitation

Precipitation scenario alteration leads to grievous ecological consequences in ecosystems,especially on the Qinghai-Tibet Plateau.Bacterial and fungal community and their abundant and rare taxa in soil ecosystems may respond differently to the changed precipitation.Therefore,more attention needs to be paid to the sensitivity of bacteria and fungi and their abundant and rare taxa to precipitation shifts.The responses of bacterial and fungal populations and their abundant and rare taxa concerning diversity,assembly,and interactions to manipulative changes of precipitation were explored via imitating no precipitation,little precipitation,and medium precipitation using 16S rRNA gene and ITS amplicon sequencing.The results indicated that the change rate of fungal Simpson diversity with precipitation was higher than that of bacteria.The slope of the modified stochasticity ratio(MST)value of fungi to precipitation was steeper than that of bacteria.The Simpson diversity and the MST value of abundant and rare taxa within bacteria had no difference with precipitation.In contrast,those of abundant taxa within fungi varied more than rare ones with precipitation.By unveiling the differential responses of microbial populations with discrepant characteristics,this study allowed us to understand the different microbial communities responding to rainfall on the Qinghai-Tibet Plateau.

The effect of long-term application of nitrogen-rich fertilizers on soil resistome:A study of conventional and organic cropping systems

Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes(ARGs)around the globe.In this study,we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices.The organic cropping system was seeded with Triticum spelta without any fertilizer.The conventional cropping system was seeded with Tríticum durum Desf and used mineral fertilizer(NPK),that resulted in an increased amount of total and available carbon and nitrogen in soils.Across all samples,we identified a total of 21 ARG classes,among which the dominant were vancomycin,tetracycline and multidrug.Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil,respectively.Correlation analysis showed significant correlations(positive and negative)among 18 genera and 6 ARGs,as well as between these ARGs and some chemical properties of soils.The analysis of metagenome-assembled genomes revealed that Nitrospirota,Thermoproteota,Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs.Collectively,the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa,including uncultivated genera,in the formation of soil resistome.

Two community types occur in gut microbiota of large-sample wild plateau pikas(Ochotona curzoniae)

Studies on large-sample gut microbial sequencing data indicate that gut microbiota can be divided into multiple community types;different community types may influence the community function and ecosystem service.However,the knowledge on the classification,diversity,interaction,and assembling of microbial community types in the gut of wild animals is still insufficient.Here,we used pika gut microbiota data as an example to study the microbial community types in large-sample sequencing dataset.Cecal microbial communities from 118 wild plateau pika(Ochotona curzoniae)individuals at 5 elevational regions on the Qinghai–Tibet Plateau were analyzed.Our results show that pika gut microbiota can be separated into 2 community types(Cluster I and Cluster II).Cluster I was mainly distributed on the high-elevation regions with more than 3694 m and was most dominated by Firmicutes.Cluster II was from the low-elevation areas(lower than 3580 m),and was predominated by Bacteroidetes.Cluster I had a higher community alpha-diversity and predicted functional diversity than Cluster II,and the betadiversity and predicted functional profiles of these 2 clusters were significantly different.Network analysis revealed that there were more complex interactions between Cluster I,which had enhanced influence on the co-occurrences of other microbes in the bacterial community when compared to Cluster II.Phylogenetic analysis found that the environmental filtering in the Cluster I was stronger than Cluster II.The assemblages of pika gut bacterial communities were determined mainly by deterministic processes,while the relative importance of deterministic processes accounted for more percentages in the Cluster I than Cluster II.Our results demonstrated that 2 gut microbial community types in pikas had distinct diversity patterns and ecological functions.Current methods are also helpful for identifying gut community types and the related mechanisms behind gut microbiota types in large-sample sequencing data of wild animals.

Altitude-dependent metabolite biomarkers reveal the mechanism of plateau pika adaptation to high altitudes

The harsh environment in the Tibetan plateau,the highest place in the world,poses thermoregulatory challenges and hypoxic stress to animals.The impacts of plateau environment on animal physiology and reproduction include external factors such as strong ultraviolet radiation and low temperature,and internal factors such as animal metabolites and gut microbiota.However,it remains unclear how plateau pika adapt to high altitudes through the combination of serum metabolites and gut microbiota.To this end,we captured 24 wild plateau pikas at the altitudes of 3400,3600,or 3800 m a.s.l.in a Tibetan alpine grassland.Using the machine learning algorithms(random forest),we identified five biomarkers of serum metabolites indicative of the altitudes,that is,dihydrotestosterone,homo-l-arginine,alpha-ketoglutaric-acid,serotonin,and threonine,which were related to body weight,reproduction,and energy metabolism of pika.Those metabolic biomarkers were positively correlated with Lachnospiraceae_Agathobacter,Ruminococcaceae,or Prevotellaceae_Prevotella,suggesting the close relationship between metabolites and gut microbiota.By identifying the metabolic biomarkers and gut microbiota analysis,we reveal the mechanisms of adaptation to high altitudes in plateau pika.

Erratum to:The fungal endophyte Epichloë gansuensis increases NaCl-tolerance in Achnatherum inebrians through enhancing the activity of plasma membrane H^(+)-ATPase and glucose-6-phosphate dehydrogenase

1.In the results,we mistakenly described the information of Figure 9B.The correct sentence should be“The factor 1 and factor 2 explained 71.30%and 16.68%of the total variance,respectively.The 0 mmol L^(-1) NaCl concentration showed the highest contribution(29.95%)to factor 1 in roots of E+plants,and 200 mmol L^(-1) NaCl concentration was significantly loaded(45.95%)on factor 2 in roots of E+plants(Figure 9B).”

The fungal endophyte Epichloëgansuensis increases NaCltolerance in Achnatherum inebrians through enhancing the activity of plasma membrane H^(+)-ATPase and glucose-6-phosphate dehydrogenase

Salt stress negatively affects plant growth,and the fungal endophyte Epichloëgansuensis increases the tolerance of its host grass species,Achnatherum inebrians,to abiotic stresses.In this work,we first evaluated the effects of E.gansuensis on glucose-6-phosphate dehydrogenase(G6PDH)and plasma membrane(PM)H^(+)-ATPase activity of Achnatherum inebrians plants under varying NaCl concentrations.Our results showed that the presence of E.gansuensis increased G6PDH,PMH^(+)-ATPase,superoxide dismutase and catalase activity to decrease O2•^(–),H_(2)O_(2)and Na^(+)contents in A.inebrians under NaCl stress,resulting in enhanced salt tolerance.In addition,the PM NADPH oxidase activity and NADPH/NADP+ratios were all lower in A.inebrians with E.ganusensis plants than A.inebrians plants without this endophyte under NaCl stress.In conclusion,E.gansuensis has a positive role in improving host grass yield under NaCl stress by enhancing the activity of G6PDH and PM H^(+)-ATPase to decrease ROS content.This provides a new way for the selection of stress-resistant and high-quality forage varieties by the use of systemic fungal endophytes.

Elymus sibiricus populations drive the community of root-associated arbuscular mycorrhizal fungi in a monoculture agroecosystem

Dear Editor,Arbuscular mycorrhizal fungi(AMF)belonging to phylum Glomeromycota,form symbiotic associations with roots of over 80%of land plant species in terrestrial ecosystems(van der Heijden et al.,2015).A growing body of evidence shows that symbiotic AMF are important for plant growth and health(van der Heijden et al.,2015).A plant root is commonly associated with a complex AMF community in terrestrial ecosystems(Pivato et al.,2007;Davison et al.,2015;Mao et al.,2015).

Characterization of a novel bifunctional enzyme from buffalo rumen metagenome and its effect on in vitro ruminal fermentation and microbial community composition

To efficiently use lignocellulosic materials in ruminants,it is crucial to explore effective enzymes,especially bifunctional enzymes.In this study,a novel stable bifunctional cellulase-xylanase protein from buffalo rumen metagenome was expressed and characterized,CelXyn2.The enzyme displayed optimal activity at pH 6.0 and 45℃.The residual endoglucanase and xylanase activities were 90.6%and 86.4%after a 60-min pre-incubation at 55℃.Hydrolysis of rice straw,wheat straw,sheepgrass and sugar beet pulp by CelXyn2 showed its ability to degrade both cellulose and hemicellulose polymers.Treatment with CelXyn2 improved the hydrolysis of agricultural residues with an evident increase in production of total gas,lactate and volatile fatty acids.The results of 16S rRNA and real-time PCR showed that the effect on in vitro ruminal microbial community depended on fermenta-tion substrates.This study demonstrated that CelXyn2 could strengthen lignocellulose hydrolysis and in vitro ruminal fermentation.These characteristics of CelXyn2 distinguish it as a promising candidate for agricultural application.