Temperature and Precipitation Drive Elevational Patterns of Microbial Beta Diversity in Alpine Grasslands.

Understanding the mechanisms underlying biodiversity patterns is a central issue in ecology, while how temperature and precipitation jointly control the elevational patterns of microbes is understudied. Here, we studied the effects of temperature, precipitation and their interactions on the alpha and beta diversity of soil archaea and bacteria in alpine grasslands along an elevational gradient of 4300-5200 m on the Tibetan Plateau. Alpha diversity was examined on the basis of species richness and evenness, and beta diversity was quantified with the recently developed metric of local contributions to beta diversity (LCBD). Typical alpine steppe and meadow ecosystems were distributed below and above 4850 m, respectively, which was consistent with the two main constraints of mean annual temperature (MAT) and mean annual precipitation (MAP). Species richness and evenness showed decreasing elevational patterns in archaea and nonsignificant or U-shaped patterns in bacteria. The LCBD of both groups exhibited significant U-shaped elevational patterns, with the lowest values occurring at 4800 m. For the three diversity metrics, soil pH was the primary explanatory variable in archaea, explaining over 20.1% of the observed variation, whereas vegetation richness, total nitrogen and the K/Al ratio presented the strongest effects on bacteria, with relative importance values of 16.1%, 12.5% and 11.6%, respectively. For the microbial community composition of both archaea and bacteria, the moisture index showed the dominant effect, explaining 17.6% of the observed variation, followed by MAT and MAP. Taken together, temperature and precipitation exerted considerable indirect effects on microbial richness and evenness through local environmental and energy supply-related variables, such as vegetation richness, whereas temperature exerted a larger direct influence on LCBD and the community composition. Our findings highlighted the profound influence of temperature and precipitation interactions on microbial beta diversity in alpine grasslands on the Tibetan Plateau.

Effect of increasing precipitation and warming on microbial community in Tibetan alpine steppe.

Soil microorganisms play an important role in regulating the feedback of Alpine steppe ecosystems to future climate change. However, the interaction effect of warming and increasing precipitation on soil microorganisms remains unclear, in the face of an ongoing warmer and wetter climate on the Tibetan Plateau. In this study, we investigate the multi-factorial effects on soil microbial diversity, community structure, and microbial interactions in a three-year climate change experiment established in an Alpine steppe on the Tibetan Plateau, involving warming (+2 °C), +15% increasing precipitation and +30% increasing precipitation. Compared to warming, warming plus increasing precipitation alleviated the decrease in microbial diversity, and increased the dissimilarities in microbial community structures, largely influenced by water and substrate availability. We further observed differences in moisture increased the differences in microbial diversity and dissimilarities in microbial community structures across different precipitation levels under ambient temperature. Interestingly, warming plus increasing precipitation could create more ecological niches for microbial species to coexist but may lessen the strength of microbial interactions in contrast to increasing precipitation alone. Collectively, our findings indicate that microbial responses to future climate change in Alpine steppe soils will be more complex than those under single-climate-factor conditions.

Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups.

The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.

Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau.

An orange pigmented, Gram-staining negative, aerobic, motile, rod-shaped bacterium isolated from a soil from the Tanggula Mountain, China was studied using a polyphasic approach. Based on 16S rRNA gene sequence similarity, strain W16RDT was found to be closely related to Sphingomonas prati DSM 103336T (99%), Sphingomonas fennica DSM 13665T (97.21%), followed by Sphingomonas laterariae DSM 25432T (96.44%), Sphingomonas haloaromaticamans CGMCC 1.10206 T (96.36%) and Sphingomonas formosensis DSM 24164T (96.06%). The strain was found to be catalase and oxidase positive and was found to grow optimally at temperatures of 20-25 °C, pH 8 and tolerated NaCl concentration up to 1% (w/v). The major fatty acids identified were summed feature eight comprising C18:1 ω 7c and/or C18:1 ω 6c (39.2%), summed feature three comprising of C16:1 ω7c and/or C16:1 ω6c (36.7%) and C16:0 (7.0%). The polar lipids detected were phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, and three unidentified lipids. The strain possessed ubiquinone-10 (Q-10) as the predominant respiratory quinone. Along with other distinguishing characteristics, we also describe the draft genome of strain W16RDT. The final assembled draft genome sequence is 3,722,743 bp with 3390 coding and 48 RNA (45 tRNA and 3 rRNA) genes. The DNA G+C content of the genomic DNA was determined to be 67%. The DNA-DNA relatedness value between the strain W16RDT and its closest phylogenetic relatives S. prati DSM 103336T, S. fennica DSM 13665T, S. laterariae DSM 25432T, and S. haloaromaticamans CGMCC 1.10206T were 52.17, 47.60, 20.93 and 17.09% respectively. The strain W16RDT could be distinguished genotypically and phenotypically from the recognized species belonging to the genus Sphingomonas and thus represents a novel species, for which the name Sphingomonas montana sp. nov. is proposed. The type strain is W16RDT (=CGMCC 1.15646T = DSM 103337T).

Pedobacterpsychrotolerans sp. nov., isolated from soil.

A Gram-stain-negative, non-motile, light-pink-pigmented, aerobic, rod-shaped bacterium, designated V5RDT, was isolated from soil of Damxung county in the Qinghai-Tibetan Plateau. Strain V5RDT grew luxuriously at 10 °C, at pH 9.0 and in the presence of 1 % NaCl (w/v). Phylogenetic analysis of 16S rRNA gene sequences placed strain V5RDT in the genus Pedobacter and found that it was most closely related to Pedobacter alluvionis DSM 19624T (97.3 %), Pedobacter ginsenosidimutans JCM 16721T (96.84 %), Pedobacter agri DSM 19486T (96.28 %), Pedobacter roseus JCM 13399T (96.22 %), Pedobacter sandarakinus KCTC 12559T (95.92 %) and Pedobacter borealis DSM 19626T (95.85 %). The G+C content of the genomic DNA of the type strain V5RDT was 37.40 mol%. DNA-DNA relatedness for the type strain V5RDT with respect to its closest phylogenetic relative, P. alluvionis DSM 19624T, was 62.5±1.7 %. The polar lipid profile of the strain consisted of phosphatidylethanolamine, one unidentified aminolipid, one unidentified glycolipid and two unidentified polar lipids. Menaquinone MK-7 was the predominant respiratory quinone, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH were the major fatty acids. With respect to phenotypic characteristics, biochemical properties and phylogenetic inference, strain V5RDT represents a novel species of the genus Pedobacter, for which the name Pedobacter psychrotolerans sp. nov is proposed. The type strain is V5RDT (=CGMCC 1.15644T=DSM 103236T).

Sphingomonas prati sp. nov., isolated from alpine meadow soil.

A Gram-staining-negative, non-motile, orange-coloured and rod-shaped aerobic bacterium, designated W18RDT, was isolated from the alpine meadow soil of the Tibetan plateau. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain W18RDT as a representative of a novel species under the genus Sphingomonas which was most closely related to Sphingomonas fennica DSM 13665T with a sequence similarity level of 97.14 %. Meanwhile, it also had a high level of sequence similarity with Sphingomonas laterariae DSM 25432T (96.51 %), Sphingomonas haloaromaticamans CGMCC 1.10206T (96.43 %) and Sphingomonas formosensis DSM 24164T (96.26 %). The G+C content of the genomic DNA of the type strain W18RDT was 66.4mol%. DNA-DNA relatedness for the type strain W18RDT with respect to its closest phylogenetic relative Sphingomonas. fennica DSM 13665Twas 21.54±1.2 %. Major cellular fatty acids in strain W18RDT were C16 : 1ω7c and/or C16 : 1ω6c (48.12 %), C18 : 1ω7c and/or C18 : 1ω6c (21.98 %) and C14 : 0 2-OH (14.93 %), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The polar lipid profile of the strain consisted of phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol and two unknown lipids. Based on the evidence from a combination of phenotypic, taxonomic and phylogenetic analyses, strain W18RDT represents a novel species of the genus Sphingomonas, for which the name Sphingomonas prati sp. nov. is proposed. The type strain is W18RDT (=CGMCC 1.15645T=DSM 103336T).

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe.

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha-1 year-1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha-1 year-1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha-1 year-1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha-1 year-1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH4+, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO2-/NH4+ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.

Warming and increased precipitation indirectly affect the composition and turnover of labile-fraction soil organic matter by directly affecting vegetation and microorganisms.

Global warming accompanied by precipitation changes impacts soil carbon sequestration. A three-year field manipulation experiment with warming (+2 °C above ambient temperature) and increased precipitation (+15% and +30% above ambient precipitation) was conducted in an alpine grassland to investigate the response of soil organic matter (SOM) to future climate change on the Qinghai-Tibet Plateau (QTP). Labile-fraction SOM (LF-SOM) fingerprints were characterized by pyrolysis-gas chromatography/tandem-mass spectrometry (Py-GC-MS/MS), and organic compounds in LF-SOM were used as indicators to quantify the contributions of vegetation input and microbial degradation to LF-SOM transformation. Increased precipitation promoted LF-SOM accumulation, which were mainly due to the positive effect of increased precipitation on vegetation productivity. Plant-derived compounds in LF-SOM (including lignin, long-chain alkyl compounds, polysaccharides and phenols) were more sensitive to increasing soil moisture than microbial-derived (including short-chain alkyl compounds, N compounds and chitin) and aromatic-derived compounds (including aromatics and polyaromatics). In contrast, warming alone intensified the effect of drought on the alpine grassland, which had negative effects on both vegetation and microorganisms and reduced LF-SOM. Warming plus increased precipitation not only alleviated the water loss caused by warming but also increased soil temperature, which was more favorable for the growth of microorganisms. This was reflected in the increase in microbial-derived compounds in LF-SOM with increasing soil temperature, which contributed to LF-SOM degradation. Aromatic-derived compounds, as refractory compounds in soil, showed no significant response to either warming or increased precipitation treatments. Acidobacteria (approximately 25%) and Actinobacteria (approximately 20%), as the dominant soil bacterial communities in the alpine grassland, were significantly correlated with plant-derived compounds. At the same time, there were significant correlations between Proteobacteria and microbial-derived compounds, as well as between Firmicutes and aromatic-derived compounds (relative abundance). Under future climate change, microbial activity will increase as temperature increases, which will promote LF-SOM degradation only if precipitation also increases.

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments.

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000-2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.