Transplants, Open Top Chambers (OTCs) and Gradient Studies Ask Different Questions in Climate Change Effects Studies

Warming-induced shifts in alpine soil microbiome: An ecosystem-scale study with environmental context-dependent insights

Climate warming is a pressing global issue with substantial impacts on soil health and function. However, the influence of environmental context on the responses of soil microorganisms to warming remains largely elusive, particularly in alpine ecosystems. This study examined the responses of the soil microbiome to in situ experimental warming across three elevations (3850 m, 4100 m, and 4250 m) in the meadow of Gongga Mountain, eastern Tibetan Plateau. Our findings demonstrate that soil microbial diversity is highly resilient to warming, with significant impacts observed only at specific elevations. Furthermore, the influence of warming on the composition of the soil microbial community is also elevation-dependent, underscoring the importance of local environmental context in shaping microbial evolution in alpine soils under climate warming. Notably, we identified soil moisture at 3850 m and carbon-to-nitrogen ratio at 4250 m as indirect predictors regulating the responses of microbial diversity to warming at specific elevations. These findings underscore the paramount importance of considering pre-existing environmental conditions in predicting the response of alpine soil microbiomes to climate warming. Our study provides novel insights into the intricate interactions between climate warming, soil microbiome, and environmental context in alpine ecosystems, illuminating the complex mechanisms governing soil microbial ecology in these fragile and sensitive environments.

Precipitation and local adaptation drive spatiotemporal variations of aboveground biomass and species richness in Tibetan alpine grasslands

The Tibetan Plateau contains the highest and largest alpine pasture in the world, which is adapted to the cold and arid climate. It is challenging to understand how the vast alpine grasslands respond to climate change. We aim to test the hypothesis that there is local adaptation in elevational populations of major plant species in Tibetan alpine grasslands, and that the spatiotemporal variations of aboveground biomass (AGB) and species richness (S) can be mainly explained by climate change only when the effect of local adaptation is removed. A 7-year reciprocal transplant experiment was conducted among the distribution center (4950 m), upper (5200 m) and lower (4650 m) limits of alpine Kobresia meadow in central Tibetan Plateau. We observed interannual variations in S and AGB of 5 functional groups and 4 major species, and meteorological factors in each of the three elevations during 2012-2018. Relationships between interannual changes of AGB and climatic factors varied greatly with elevational populations within a species. Elevation of population origin generally had a greater or an equal contribution to interannual variation in AGB of the 4 major species, compared to temperature and precipitation effects. While the effect of local adaptation was removed by calculating differences in AGB and S between elevations of migration and origin, relative changes in AGB and S were mainly explained by precipitation change rather than by temperature change. Our data support the hypothesis, and further provide evidence that the monsoon-adapted alpine grasslands are more sensitive to precipitation change than to warming.

Fungal communities in European alpine soils are not affected by short-term in situ simulated warming than bacterial communities

The impact of global warming on biological communities colonizing European alpine ecosystems was recently studied. Hexagonal open top chambers (OTCs) were used for simulating a short-term in situ warming (estimated around 1°C) in some alpine soils to predict the impact of ongoing climate change on resident microbial communities. Total microbial DNA was extracted from soils collected either inside or outside the OTCs over 3 years of study. Bacterial and fungal rRNA copies were quantified by qPCR. Metabarcoding sequencing of taxonomy target genes was performed (Illumina MiSeq) and processed by bioinformatic tools. Alpha- and beta-diversity were used to evaluate the structure of bacterial and fungal communities. qPCR suggests that, although fluctuations have been observed between soils collected either inside and outside the OTCs, the simulated warming induced a significant (p < 0.05) shift only for bacterial abundance. Likewise, significant (p < 0.05) changes in bacterial community structure were detected in soils collected inside the OTCs, with a clear increase of oligotrophic taxa. On the contrary, fungal diversity of soils collected either inside and outside the OTCs did not exhibit significant (p < 0.05) differences, suggesting that the temperature increase in OTCs compared to ambient conditions was not sufficient to change fungal communities.

Lowland plant arrival in alpine ecosystems facilitates a decrease in soil carbon content under experimental climate warming

Climate warming is releasing carbon from soils around the world^1-3, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems^4-9. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown¹⁰. Here we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% ± 31% (mean ± 95% CIs) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration and CO₂ release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics.

Interspecific trait variability and local soil conditions modulate grassland model community responses to climate

Medium‐to‐high elevation grasslands provide critical services in agriculture and ecosystem stabilization, through high biodiversity and providing food for wildlife. However, these ecosystems face elevated risks of disruption due to predicted soil and climate changes. Separating the effects of soil and climate, however, is difficult in situ, with previous experiments focusing largely on monocultures instead of natural grassland communities. We experimentally exposed model grassland communities, comprised of three species grown on either local or reference soil, to varied climatic environments along an elevational gradient in the European Alps, measuring the effects on species and community traits. Although species‐specific biomass varied across soil and climate, species' proportional contributions to community‐level biomass production remained consistent. Where species experienced low survivorship, species‐level biomass production was maintained through increased productivity of surviving individuals; however, maximum species‐level biomass was obtained under high survivorship. Species responded directionally to climatic variation, spatially separating differentially by plant traits (including height, reproduction, biomass, survival, leaf dry weight, and leaf area) consistently across all climates. Local soil variation drove stochastic trait responses across all species, with high levels of interactions occurring between site and species. This soil variability obscured climate‐driven responses: we recorded no directional trait responses for soil‐corrected traits like observed for climate‐corrected traits. Our species‐based approach contributes to our understanding of grassland community stabilization and suggests that these communities show some stability under climatic variation.

Decreased bee emergence along an elevation gradient: Implications for climate change revealed by a transplant experiment

Bees experience differences in thermal tolerance based on their geographical range; however, there are virtually no studies that examine how overwintering temperatures may influence immature survival rates. Here, we conducted a transplant experiment along an elevation gradient to test for climate-change effects on immature overwinter survival using movement along elevational gradient for a community of 26 cavity-nesting bee species in the family Megachilidae along the San Francisco Peaks, Arizona elevational gradient. In each of three years, we placed nest blocks at three elevations, to be colonized by native Megachilidae. Colonized blocks were then (1) moved to lower (warmer) elevations; (2) moved to higher (cooler) elevations; or (3) left in their natal habitat (no change in temperature). Because Megachilidae occupy high elevations with colder temperatures more than any other family of bees, we predicted that emergence would decrease in nest blocks moved to lower elevations, but that we would find no differences in emergence when nest blocks were moved to higher elevations. We found three major results: (1) Bee species moved to lower (warmer) habitats exhibited a 30% decrease in emergence compared with species moved within their natal habitat. (2) Habitat generalists were more likely than habitat specialists to emerge when moved up or down in elevation regardless of their natal life zones. (3) At our highest elevation treatment, emergence increased when blocks were moved to higher elevations, indicating that at least some Megachilidae species can survive at colder temperatures. Our results suggest that direct effects of warming temperatures will have negative impacts on the overall survival of Megachilidae. Additionally, above the tree line, low availability of wood-nesting resources is a probable limiting factor on bees moving up in elevation.

Microclimatic Warming Leads to a Decrease in Species and Growth Form Diversity: Insights From a Tropical Alpine Grassland

Due to warming, changes in microclimatic temperatures have shifted plant community structure and dynamics in tundra and alpine regions. The directionality and magnitude of these changes are less known for tropical alpine ecosystems. To understand the likely trajectory of these shifts in the Andes, we conducted a warming experiment in the northern Andes—using open-top chambers (OTC). In this study, we ask (1) how do OTCs affect air and soil temperatures in microclimates of tropical alpine regions, year-round and during the dry season? (2) What are the effects of 7 years of warming on (a) the aboveground biomass (AGB) and (b) the plant taxonomic and growth form diversity? We installed five monitoring blocks in 2012 at ca. 4,200 m asl with 20 OTCs and 50 control plots randomly distributed within each block. We measured AGB, plant community diversity, and growth form diversity between 2014 and 2019. After 7 years of warming, we found significant increases in mean monthly (+0.24°C), daily (+0.16°C), and night air temperatures (+0.33°C) inside the OTCs, and the OTCs intensified microclimatic conditions during the dry season. Additionally, OTCs attenuated extreme temperatures—particularly in the soil—and the number of freezing events. AGB significantly increased in OTCs, and by 2019, it was 27% higher in OTCs than in control. These changes were driven mainly by a progressive increment of tussock grasses such as Calamagrostis intermedia, typical of lower elevations. The increase of tussocks led to a significant decrease in species diversity and evenness inside OTCs, but not in species richness after accounting by sampling time. Furthermore, cushions and herbs decreased inside OTCs. Our results show that experimental warming using OTCs in equatorial regions leads to decreased daily thermal amplitude and night temperatures rather than the level of increase in mean temperatures observed in temperate regions. The increase of tussocks and decrease in diversity of species and growth forms due to prolonged modifications in microclimatic temperature might be a step toward shrub-dominated ecosystems. Further research on this topic would help understand shifts in growth form dominance and the direction and rate of change of the system.

Hundreds of nuclear and plastid loci yield novel insights into orchid relationships

PREMISE

The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed.

METHODS

We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses.

RESULTS

Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes.

CONCLUSIONS

Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.

The response of culturally important plants to experimental warming and clipping in Pakistan Himalayas

The relative effects of climate warming with grazing on medicinally important plants are not fully understood in Hindukush-Himalaya (HKH) region. Therefore, we combined the indigenous knowledge about culturally important therapeutic plants and climate change with experimental warming (open-top chambers) and manual clipping (simulated grazing effect) and compared the relative difference on aboveground biomass and percent cover of plant species at five alpine meadow sites on an elevation gradient (4696 m-3346 m) from 2016-2018. Experimental warming increased biomass and percent cover throughout the experiment. However, the interactive treatment effect (warming x clipping) was significant on biomass but not on percent cover. These responses were taxa specific. Warming induced an increase of 1 ± 0.6% in Bistorta officinalis percent cover while for Poa alpina it was 18.7 ± 4.9%. Contrastingly, clipping had a marginally significant effect in reducing the biomass and cover of all plant species. Clipping treatment reduced vegetation cover & biomass by 2.3% and 6.26%, respectively, but that was not significant due to the high variability among taxa response at different sites. It was found that clipping decreased the effects of warming in interactive plots. Thus, warming may increase the availability of therapeutic plants for indigenous people while overgrazing would have deteriorating effects locally. The findings of this research illustrate that vegetation sensitivity to warming and overgrazing is likely to affect man-environment relationships, and traditional knowledge on a regional scale.

Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.

Effects of ambient climate and three warming treatments on fruit production in an alpine, subarctic meadow community

PREMISE

Climate change is having major impacts on alpine and arctic regions, and inter-annual variations in temperature are likely to increase. How increased climate variability will impact plant reproduction is unclear.

METHODS

In a 4-year study on fruit production by an alpine plant community in northern Sweden, we applied three warming regimes: (1) a static level of warming with open-top chambers (OTC), (2) press warming, a yearly stepwise increase in warming, and (3) pulse warming, a single-year pulse event of higher warming. We analyzed the relationship between fruit production and monthly temperatures during the budding period, fruiting period, and whole fruit production period and the effect of winter and summer precipitation on fruit production.

RESULTS

Year and treatment had a significant effect on total fruit production by evergreen shrubs, Cassiope tetragona, and Dryas octopetala, with large variations between treatments and years. Year, but not treatment, had a significant effect on deciduous shrubs and graminoids, both of which increased fruit production over the 4 years, while forbs were negatively affected by the press warming, but not by year. Fruit production was influenced by ambient temperature during the previous-year budding period, current-year fruiting period, and whole fruit production period. Minimum and average temperatures were more important than maximum temperature. In general, fruit production was negatively correlated with increased precipitation.

CONCLUSIONS

These results indicate that predicted increased climate variability and increased precipitation due to climate change may affect plant reproductive output and long-term community dynamics in alpine meadow communities.

Plant traits and vegetation data from climate warming experiments along an 1100 m elevation gradient in Gongga Mountains, China

Functional trait data enhance climate change research by linking climate change, biodiversity response, and ecosystem functioning, and by enabling comparison between systems sharing few taxa. Across four sites along a 3000–4130 m a.s.l. gradient spanning 5.3 °C in growing season temperature in Mt. Gongga, Sichuan, China, we collected plant functional trait and vegetation data from control plots, open top chambers (OTCs), and reciprocally transplanted vegetation turfs. Over five years, we recorded vascular plant composition in 140 experimental treatment and control plots. We collected trait data associated with plant resource use, growth, and life history strategies (leaf area, leaf thickness, specific leaf area, leaf dry matter content, leaf C, N and P content and C and N isotopes) from local populations and from experimental treatments. The database consists of 6,671 plant records and 36,743 trait measurements (increasing the trait data coverage of the regional flora by 500%) covering 11 traits and 193 plant taxa (ca. 50% of which have no previous published trait data) across 37 families.

Measurement(s)	leaf growth and development trait • Abundance • leaf area trait • leaf composition trait • leaf morphology trait • Vascular Plant • total biomass yield • climate
Technology Type(s)	balance • visual observation method • Scanner Device • leaf stoichiometry and isotope assays • weather station
Factor Type(s)	plants • temperature • plant functional traits (specific leaf area, leaf dry matter content, leaf carbon content, leaf nitrogen content, leaf size, leaf thickness) • type of treatment (e.g in situ warming experiments using an Open Top Chamber)
Sample Characteristic - Organism	Tracheophyta
Sample Characteristic - Environment	area of sedge- and forb-dominated herbaceous vegetation
Sample Characteristic - Location	Ganzi Tibetan Autonomous Prefecture

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12033786

Light and warming drive forest understorey community development in different environments

Plant community composition and functional traits respond to chronic drivers such as climate change and nitrogen (N) deposition. In contrast, pulse disturbances from ecosystem management can additionally change resources and conditions. Community responses to combined environmental changes may further depend on land-use legacies. Disentangling the relative importance of these global change drivers is necessary to improve predictions of future plant communities. We performed a multifactor global change experiment to disentangle drivers of herbaceous plant community trajectories in a temperate deciduous forest. Communities of five species, assembled from a pool of 15 forest herb species with varying ecological strategies, were grown in 384 mesocosms on soils from ancient forest (forested at least since 1850) and postagricultural forest (forested since 1950) collected across Europe. Mesocosms were exposed to two-level full-factorial treatments of warming, light addition (representing changing forest management) and N enrichment. We measured plant height, specific leaf area (SLA) and species cover over the course of three growing seasons. Increasing light availability followed by warming reordered the species towards a taller herb community, with limited effects of N enrichment or the forest land-use history. Two-way interactions between treatments and incorporating intraspecific trait variation (ITV) did not yield additional inference on community height change. Contrastingly, community SLA differed when considering ITV along with species reordering, which highlights ITV's importance for understanding leaf morphology responses to nutrient enrichment in dark conditions. Contrary to our expectations, we found limited evidence of land-use legacies affecting community responses to environmental changes, perhaps because dispersal limitation was removed in the experimental design. These findings can improve predictions of community functional trait responses to global changes by acknowledging ITV, and subtle changes in light availability. Adaptive forest management to impending global change could benefit the restoration and conservation of understorey plant communities by reducing the light availability.

Warming Increases Pollen Lipid Concentration in an Invasive Thistle, with Minor Effects on the Associated Floral-Visitor Community

Climate warming is likely to change the ways in which plants interact with their insect mutualists, for example through changes in phytochemistry. In particular, this may have implications for the ways in which we manage noxious weeds, which may spread more quickly if they experience stronger mutualistic interactions. We grew the invasive nodding thistle, Carduus nutans, in two experimental treatments in the field: either passively warmed with open top chambers or at ambient temperatures. We collected pollen from thistles in each treatment and analysed the total protein, lipid, and carbohydrate content. We observed no difference in the pollen protein or carbohydrate content, but the total lipid content of the pollen was significantly higher in warmed plants. We conducted a total of 12.75 h of observations of putatively mutualistic, flower-visiting insects. In addition, we spent 4.17 h collecting bees that visited thistle inflorescences in the treatments, allowing us to identify them to species. We found a significant increase in the abundance of flower-visiting insects in the observations, but not bee abundance in collections. In addition, there was no treatment effect on the number of flower-visiting morphotypes in the observations, or bee species richness in the collections. However, a nonparametric test did identify a significant effect of warming on the composition of flower-visiting morphotypes in observations and bee species in collections. Overall, the warming treatment significantly increased lipid content of the pollen, but had relatively weak effects on insect visitation patterns. However, these effects may be amplified at larger spatial and temporal scales or higher temperatures.