Decreased growth of wild soil microbes after 15 years of transplant-induced warming in a montane meadow

Temperature fluctuation in soil alters the nanoplastic sensitivity in wheat

Despite the wide acknowledgment that plastic pollution and global warming have become serious agricultural concerns, their combined impact on crop growth remains poorly understood. Given the unabated megatrend, a simulated soil warming (SWT, +4 °C) microcosm experiment was carried out to provide a better understanding of the effects of temperature fluctuations on wheat seedlings exposed to nanoplastics (NPs, 1 g L-1 61.71 ± 0.31 nm polystyrene). It was documented that SWT induced oxidative stress in wheat seedlings grown in NPs-contaminated soil, with an 85.56 % increase in root activity, while decreasing plant height, fresh weight, and leaf area by 8.72 %, 47.68 %, and 15.04 % respectively. The SWT also resulted in reduced photosynthetic electron-transfer reaction and Calvin-Benson cycle in NPs-treated plants. Under NPs, SWT stimulated the tricarboxylic acid (TCA) metabolism and bio-oxidation process. The decrease in photosynthesis and the increase in respiration resulted in an 11.94 % decrease in net photosynthetic rate (Pn). These results indicated the complicated interplay between climate change and nanoplastic pollution in crop growth and underscored the potential risk of nanoplastic pollution on crop production in the future climate.

Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment

Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the 18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members in Solirubrobacter and Pseudonocardia genera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors.

Soil warming increases the number of growing bacterial taxa but not their growth rates

Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.

Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency

Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.

Rapid growth rate responses of terrestrial bacteria to field warming on the Antarctic Peninsula

Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site-likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink-indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing

BACKGROUND

We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.

RESULTS

An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.

CONCLUSIONS

The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.

Soil microbiome feedback to climate change and options for mitigation

Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO₂ and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.

Distinct Growth Responses of Tundra Soil Bacteria to Short-Term and Long-Term Warming

Increases in Arctic temperatures have thawed permafrost and accelerated tundra soil microbial activity, releasing greenhouse gases that amplify climate warming. Warming over time has also accelerated shrub encroachment in the tundra, altering plant input abundance and quality, and causing further changes to soil microbial processes. To better understand the effects of increased temperature and the accumulated effects of climate change on soil bacterial activity, we quantified the growth responses of individual bacterial taxa to short-term warming (3 months) and long-term warming (29 years) in moist acidic tussock tundra. Intact soil was assayed in the field for 30 days using ¹⁸O-labeled water, from which taxon-specific rates of ¹⁸O incorporation into DNA were estimated as a proxy for growth. Experimental treatments warmed the soil by approximately 1.5°C. Short-term warming increased average relative growth rates across the assemblage by 36%, and this increase was attributable to emergent growing taxa not detected in other treatments that doubled the diversity of growing bacteria. However, long-term warming increased average relative growth rates by 151%, and this was largely attributable to taxa that co-occurred in the ambient temperature controls. There was also coherence in relative growth rates within broad taxonomic levels with orders tending to have similar growth rates in all treatments. Growth responses tended to be neutral in short-term warming and positive in long-term warming for most taxa and phylogenetic groups co-occurring across treatments regardless of phylogeny. Taken together, growing bacteria responded distinctly to short-term and long-term warming, and taxa growing in each treatment exhibited deep phylogenetic organization. IMPORTANCE Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. In response to our warming treatments, tundra soil bacteria grew faster, consistent with increased rates of decomposition and carbon flux to the atmosphere. Our findings suggest that bacterial growth rates may continue to increase in the coming decades as faster growth is driven by the accumulated effects of long-term warming. Observed phylogenetic organization of bacterial growth rates may also permit taxonomy-based predictions of bacterial responses to climate change and inclusion into ecosystem models.

Elevated temperature and CO2 strongly affect the growth strategies of soil bacteria

The trait-based strategies of microorganisms appear to be phylogenetically conserved, but acclimation to climate change may complicate the scenario. To study the roles of phylogeny and environment on bacterial responses to sudden moisture increases, we determine bacterial population-specific growth rates by ¹⁸O-DNA quantitative stable isotope probing (¹⁸O-qSIP) in soils subjected to a free-air CO₂ enrichment (FACE) combined with warming. We find that three growth strategies of bacterial taxa - rapid, intermediate and slow responders, defined by the timing of the peak growth rates - are phylogenetically conserved, even at the sub-phylum level. For example, members of class Bacilli and Sphingobacteriia are mainly rapid responders. Climate regimes, however, modify the growth strategies of over 90% of species, partly confounding the initial phylogenetic pattern. The growth of rapid bacterial responders is more influenced by phylogeny, whereas the variance for slow responders is primarily explained by environmental conditions. Overall, these results highlight the role of phylogenetic and environmental constraints in understanding and predicting the growth strategies of soil microorganisms under global change scenarios.

Scientists' warning of threats to mountains

Mountains are an essential component of the global life-support system. They are characterized by a rugged, heterogenous landscape with rapidly changing environmental conditions providing myriad ecological niches over relatively small spatial scales. Although montane species are well adapted to life at extremes, they are highly vulnerable to human derived ecosystem threats. Here we build on the manifesto 'World Scientists' Warning to Humanity', issued by the Alliance of World Scientists, to outline the major threats to mountain ecosystems. We highlight climate change as the greatest threat to mountain ecosystems, which are more impacted than their lowland counterparts. We further discuss the cascade of "knock-on" effects of climate change such as increased UV radiation, altered hydrological cycles, and altered pollution profiles; highlighting the biological and socio-economic consequences. Finally, we present how intensified use of mountains leads to overexploitation and abstraction of water, driving changes in carbon stock, reducing biodiversity, and impacting ecosystem functioning. These perturbations can provide opportunities for invasive species, parasites and pathogens to colonize these fragile habitats, driving further changes and losses of micro- and macro-biodiversity, as well further impacting ecosystem services. Ultimately, imbalances in the normal functioning of mountain ecosystems will lead to changes in vital biological, biochemical, and chemical processes, critically reducing ecosystem health with widespread repercussions for animal and human wellbeing. Developing tools in species/habitat conservation and future restoration is therefore essential if we are to effectively mitigate against the declining health of mountains.

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

BACKGROUND

Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.

RESULTS

Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to ¹³C-AMF hyphosphere DNA from a ¹³CO₂ plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% ¹³C), even though the soils' overall enrichment was low (1.8 atom% ¹³C). We assembled 212 ¹³C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived ¹³C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.

CONCLUSIONS

Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.

Embracing mountain microbiome and ecosystem functions under global change

Mountains are pivotal to maintaining habitat heterogeneity, global biodiversity, ecosystem functions and services to humans. They have provided classic model natural systems for plant and animal diversity gradient studies for over 250 years. In the recent decade, the exploration of microorganisms on mountainsides has also achieved substantial progress. Here, we review the literature on microbial diversity across taxonomic groups and ecosystem types on global mountains. Microbial community shows climatic zonation with orderly successions along elevational gradients, which are largely consistent with traditional climatic hypotheses. However, elevational patterns are complicated for species richness without general rules in terrestrial and aquatic environments and are driven mainly by deterministic processes caused by abiotic and biotic factors. We see a major shift from documenting patterns of biodiversity towards identifying the mechanisms that shape microbial biogeographical patterns and how these patterns vary under global change by the inclusion of novel ecological theories, frameworks and approaches. We thus propose key questions and cutting-edge perspectives to advance future research in mountain microbial biogeography by focusing on biodiversity hypotheses, incorporating meta-ecosystem framework and novel key drivers, adapting recently developed approaches in trait-based ecology and manipulative field experiments, disentangling biodiversity-ecosystem functioning relationships and finally modelling and predicting their global change responses.