The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization

Low Carbon Loss from Long-Term Manure-Applied Soil during Abrupt Warming Is Realized through Soil and Microbiome Interplay

Manure application is a global approach for enhancing soil organic carbon (SOC) sequestration. However, the response of SOC decomposition in manure-applied soil to abrupt warming, often occurring during diurnal temperature fluctuations, remains poorly understood. We examined the effects of long-term (23 years) continuous application of manure on SOC chemical composition, soil respiration, and microbial communities under temperature shifts (15 vs 25 °C) in the presence of plant residues. Compared to soil without fertilizer, manure application reduced SOC recalcitrance indexes (i.e., aliphaticity and aromaticity) by 17.45 and 21.77%, and also reduced temperature sensitivity (Q10) of native SOC decomposition, plant residue decomposition, and priming effect by 12.98, 15.98, and 52.83%, respectively. The relative abundances of warm-stimulated chemoheterotrophic bacteria and fungi were lower in the manure-applied soil, whereas those of chemoautotrophic Thaumarchaeota were higher. In addition, the microbial network of the manure-applied soil was more interconnected, with more negative connections with the warm-stimulated taxa than soils without fertilizer or with chemical fertilizer applied. In conclusion, our study demonstrated that the reduced loss of SOC to abrupt warming by manure application arises from C chemistry modification, less warm-stimulated microorganisms, a more complex microbial community, and the higher CO2 intercepting capability by Thaumarchaeota.

Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China

The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.

Contrasting responses of α- and β-multifunctionality to aboveground plant community in the Qinghai-Tibet Plateau

The aboveground plant communities are crucial in driving ecosystem functioning, particularly being the primary producers in terrestrial ecosystems. Numerous studies have investigated the impacts of aboveground plant communities on multiple ecosystem functions at α-scale. However, such critical effects have been unexplored at β-scale and the comparative assessment of the effects and underlying mechanisms of aboveground plant communities on α- and β-multifunctionality has been lacking. In this study, we examined the effects of aboveground plant communities on soil multifunctionality both at α- and β-scale in the alpine meadow of the Tibetan Plateau. Additionally, we quantified the direct effects of aboveground plant communities, as well as the indirect effects mediated by changes in biotic and abiotic factors, on soil multifunctionality at both scales. Our findings revealed that: 1) Aboveground plant communities had significantly positive effects on α-multifunctionality whereas, β-multifunctionality was not affected significantly. 2) Aboveground plant communities directly influence α- and β-multifunctionality in contrasting ways, with positive and negative effects, respectively. Apart from the direct effects of plant community, we found that soil water content and bacterial β-diversity serving as the primary predictors for the responses of α- and β-multifunctionality to the presence of aboveground plant communities, respectively. And β-soil biodiversity appeared to be a stronger predictor of multifunctionality relative to α-soil biodiversity. Our findings provide novel insights into the drivers of ecosystem multifunctionality at different scales, highlight the importance of maintaining biodiversity at multiple scales and offer valuable knowledge for the maintenance of ecosystem functioning and the restoration of alpine meadow ecosystems.

Deciphering variations in the surficial bacterial compositions and functional profiles in the intersection between North and South Yellow Sea

The coastal ocean systems play paramount role in the nutrient biogeochemistry because of its interconnected environment. To gain a novel insight into coupling relationships between bacterial community, functioning properties and nutrient metabolism, we conducted analysis on the patterns and driving factors of planktonic bacterial functional community across subsurface water of marine ranching near the Yellow Sea in both summer and winter. Illumina HiSeq Sequencing and a corresponding set of biogeochemical data were used to assess distribution patterns of taxa, adaptive mechanism and metabolic function. Results demonstrated that Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota were dominant phyla both in summer and winter. Taxonomic profiles related to nutrient variation were found to be highly correlated with Dissolved Oxygen (DO) and Chlorophyll fluorescence (FLUO), and distinct diversity differences were also found between summer and winter samples. Functional activity in summer associated with the relative abundance of phototrophy and photoautotrophy were the highest in the subsurface water, while in winter the dominant functional properties were mainly include chemoheterotrophy and aerobic_ chemoheterotrophy. A significant difference related to functional activity between summer and winter, mainly representing ligninolysis and iron_respiration. In general, our study provides a framework for understanding the relative importance of environmental factors, temperature variation and nutrient availability in shaping the metabolic processes of aquatic microorganisms, particularly in ocean mariculture systems.

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.

Key Role of Vegetation Cover in Alleviating Microplastic-Enhanced Carbon Emissions

Microplastics (MPs) are considered to influence fundamental biogeochemical processes, but the effects of plant residue-MP interactions on soil carbon turnover in urban greenspaces are virtually unknown. Here, an 84-day incubation experiment was constructed using four types of single-vegetation-covered soils (6 years), showing that polystyrene MP (PSMP) pollution caused an unexpectedly large increase in soil CO2 emissions. The additional CO2 originating from highly bioavailable active dissolved organic matter molecules (<380 °C, predominantly polysaccharides) was converted from persistent carbon (380-650 °C, predominantly aromatic compounds) rather than PSMP derivatives. However, the priming effect of PSMP derivatives was weakened in plant-driven soils (resistivity: shrub > tree > grass). This can be explained from two perspectives: (1) Plant residue-driven humification processes reduced the percentage of bioavailable active dissolved organic matter derived from the priming effects of PSMPs. (2) Plant residues accelerated bacterial community succession (dominated by plant residue types) but slowed fungal community demise (retained carbon turnover-related functional taxa), enabling specific enrichment of glycolysis, the citric acid cycle and the pentose phosphate pathway. These results provide a necessary theoretical basis to understand the role of plant residues in reducing PSMP harm at the ecological level and refresh knowledge about the importance of biodiversity for ecosystem stability.

Soil microbial responses to simulated climate change across polar ecosystems

The polar regions are among the most biologically constrained in the world, characterized by cold temperatures and reduced liquid water. These limitations make them among the most climate-sensitive regions on Earth. Despite the overwhelming constraints from low temperatures and resource availability, many polar ecosystems, including polar deserts and tundras across the Arctic and Antarctic host uniquely diverse microbial communities. Polar regions have warmed more rapidly than the global average, with continued warming predicted for the future, which will reduce constraints on soil microbial activity. This could alter polar carbon (C) cycles, increasing CO2 emissions into the atmosphere. The objective of this study was to determine how increased temperature and moisture availability impacts microbial respiration in polar regions, by focusing on a diversity of ecosystem types (polar desert vs. tundra) that are geographically distant across Antarctica and the Arctic. We found that polar desert soil microbes were co-limited by temperature and moisture, though C and nitrogen (N) mineralization were only stimulated at the coldest and driest of the two polar deserts. Only bacterial biomass was impacted at the less harsh of the polar deserts, suggesting microbial activity is limited by factors other than temperature and moisture. Of the tundra sites, only the Antarctic tundra was climate-sensitive, where increased temperature decreased C and N mineralization while water availability stimulated it. The greater availability of soil resources and vegetative biomass at the Arctic tundra site might lead to its lack of climate-sensitivity. Notably, while C and N dynamics were climate-sensitive at some of our polar sites, P availability was not impacted at any of them. Our results demonstrate that soil microbial processes in some polar ecosystems are more sensitive to changes in temperature and moisture than others, with implications for soil C and N storage that are not uniformly predictable across polar regions.

Spatio-temporal distribution characteristics and influencing factors of protoporphyrin IX in the estuarine-coastal ecosystems

Protoporphyrin IX (PPIX), a key precursor for the synthesis of chlorophyll and heme, is fundamental to photosynthetic eukaryotic cells and participates in light absorption, energy transduction, and numerous other cellular metabolic activities. Along with the application of genetic and biochemical techniques over the past few years, our understanding of the formation of PPIX has been largely advanced, especially regarding possible metabolic pathways. However, the ecological role and function of PPIX in natural ecosystems remains unclear. We have previously established a method for quantifying PPIX in marine ecosystems. Here, our results provide evidence that PPIX is not only subtly linked to nutrient uptake but also triggers phytoplankton productivity. PPIX and its derivatives are dynamic spatiotemporally in direct response to increased nutrient availability. Using 16 S rRNA gene amplicon sequencing, PPIX was revealed to interact strongly with many microorganisms, indicating that PPIX serves as a critical metabolite in maintaining microbial metabolism and community development. In summary, we observed that PPIX is linearly related to nutrient availability and microbial diversity. The levels of microbial PPIX reflect ecological health, and the availability of PPIX and nutrients jointly affect microbial community composition.

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.

Responses of soil microbes and enzymes to long-term warming incubation in different depths of permafrost peatland soil

Soil microbes and enzymes mediate soil carbon-climate feedback, and their responses to increasing temperature partly affect soil carbon stability subjected to the effects of climate change. We performed a 50-month incubation experiment to determine the effect of long-term warming on soil microbes and enzymes involved in carbon cycling along permafrost peatland profile (0-150 cm) and investigated their response to water flooding in the active soil layer. Soil bacteria, fungi, and most enzymes were observed to be sensitive to changes in temperature and water in the permafrost peatland. Bacterial and fungal abundance decreased in the active layer soil but increased in the deepest permafrost layer under warming. The highest decrease in the ratio of soil bacteria to fungi was observed in the deepest permafrost layer under warming. These results indicated that long-term warming promotes recalcitrant carbon loss in permafrost because fungi are more efficient in decomposing high-molecular-weight compounds. Soil microbial catabolic activity measured using Biolog Ecoplates indicated a greater degree of average well color development at 15 °C than at 5 °C. The highest levels of microbial catabolic activity, functional diversity, and carbon substrate utilization were found in the permafrost boundary layer (60-80 cm). Soil polyphenol oxidase that degrades recalcitrant carbon was more sensitive to increases in temperature than β-glucosidase, N-acetyl-β-glucosaminidase, and acid phosphatase, which degrade labile carbon. Increasing temperature and water flooding exerted a synergistic effect on the bacterial and fungal abundance and β-glucosidase, acid phosphatase, and RubisCO activity in the topsoil. Structural equation modeling analysis indicated that soil enzyme activity significantly correlated with ratio of soil bacteria to fungi and microbial catabolic activity. Our results provide valuable insights into the linkage response of soil microorganisms, enzymes to climate change and their feedback to permafrost carbon loss.

Genome analysis of a plasmid-bearing myxobacterim Myxococcus sp. strain MxC21 with salt-tolerant property

Myxobacteria are widely distributed in various habitats of soil and oceanic sediment. However, it is unclear whether soil-dwelling myxobacteria tolerate a saline environment. In this study, a salt-tolerant myxobacterium Myxococcus sp. strain MxC21 was isolated from forest soil with NaCl tolerance >2% concentration. Under 1% salt-contained condition, strain MxC21 could kill and consume bacteria prey and exhibited complex social behaviors such as S-motility, biofilm, and fruiting body formation but adopted an asocial living pattern with the presence of 1.5% NaCl. To investigate the genomic basis of stress tolerance, the complete genome of MxC21 was sequenced and analyzed. Strain MxC21 consists of a circular chromosome with a total length of 9.13 Mbp and a circular plasmid of 64.3 kb. Comparative genomic analysis revealed that the genomes of strain MxC21 and M. xanthus DK1622 share high genome synteny, while no endogenous plasmid was found in DK1622. Further analysis showed that approximately 21% of its coding genes from the genome of strain MxC21 are predominantly associated with signal transduction, transcriptional regulation, and protein folding involved in diverse niche adaptation such as salt tolerance, which enables social behavior such as gliding motility, sporulation, and predation. Meantime, a high number of genes are also found to be involved in defense against oxidative stress and production of antimicrobial compounds. All of these functional genes may be responsible for the potential salt-toleration. Otherwise, strain MxC21 is the second reported myxobacteria containing indigenous plasmid, while only a small proportion of genes was specific to the circular plasmid of strain MxC21, and most of them were annotated as hypothetical proteins, which may have a direct relationship with the habitat adaptation of strain MxC21 under saline environment. This study provides an inspiration of the adaptive evolution of salt-tolerant myxobacterium and facilitates a potential application in the improvement of saline soil in future.

Effects of Microplastics on Soil Carbon Mineralization: The Crucial Role of Oxygen Dynamics and Electron Transfer

Although our understanding of the effects of microplastics on the dynamics of soil organic matter (SOM) has considerably advanced in recent years, the fundamental mechanisms remain unclear. In this study, we examine the effects of polyethylene and poly(lactic acid) microplastics on SOM processes via mineralization incubation. Accordingly, we evaluated the changes in carbon dioxide (CO2) and methane (CH4) production. An O2 planar optical sensor was used to detect the temporal behavior of dissolved O2 during incubation to determine the microscale oxygen heterogeneity caused by microplastics. Additionally, the changes in soil dissolved organic matter (DOM) were evaluated using a combination of spectroscopic approaches and ultrahigh-resolution mass spectrometry. Microplastics increased cumulative CO2 emissions by 160-613%, whereas CH4 emissions dropped by 45-503%, which may be attributed to the oxygenated porous habitats surrounding microplastics. Conventional and biodegradable microplastics changed the quantities of soil dissolved organic carbon. In the microplastic treatments, DOM with more polar groups was detected, suggesting a higher level of electron transport. In addition, there was a positive correlation between the carbon concentration, electron-donating ability, and CO2 emission. These findings suggest that microplastics may facilitate the mineralization of SOM by modifying O2 microenvironments, DOM concentration, and DOM electron transport capability. Accordingly, this study provides new insights into the impact of microplastics on soil carbon dynamics.

Reduced Arbuscular Mycorrhizal Fungi (AMF) Diversity in Light and Moderate Fire Sites in Taiga Forests, Northeast China

Forest fires are an important disturbance factor in forest ecosystems, and obviously change the soil environment. Arbuscular mycorrhizal fungi, as a medium and bridge between vegetation and soil, play a crucial role in mediating plant nutrient uptake and regulating the productivity, stability, and succession of vegetation-soil systems. To investigate the effects of forest fires on the community structure and diversity of arbuscular mycorrhizal fungi in cold-temperate Larix gmelinii forests, we collected soils from light, moderate, and heavy fire disturbance forests and a natural forest as a control forest in Greater Khingan Larix gmelinii forests, in the northeast of China. The community structure and diversity of arbuscular mycorrhizal fungi was sequenced using Illumina MiSeq technology and we analyzed the correlation with the soil physicochemical characteristics. The results showed that the contents of microbial biomass content (MBC), moisture content (MC), total nitrogen (TN), and available phosphors (AP) increased significantly (p < 0.05) with increasing fire intensity (from Light to heavy fire), but available potassium (AK) decreased significantly (p < 0.05). These changes were not significant. A total of 14,554 valid sequences from all sequences were classified into 66 ASVs that belonged into one phylum, one order, four families, and four genera. The genera included Glomus, Ambispora, Paraglomus, and Acaulospora, and Glomus was the dominant genus (the genera with the five most relative abundances) in the control and heavy-fire forests. Non-metric multidimensional scaling (NMDS) analysis showed that forest fires significantly affected the community structure of arbuscular mycorrhizal fungi (p < 0.01). Redundancy analysis (RDA) showed that MBC, SOC, and AP contents significantly affected the composition structure and diversity of arbuscular mycorrhizal fungi communities. This study indicated that forest fires affected the composition and diversity of soil arbuscular mycorrhizal fungi communities through changing the soil physicochemical parameters (MBC, SOC, and AP) in cold-temperate Larix gmelinii forests. The study of soil physicochemical properties and arbuscular mycorrhizal fungi diversity in cold-temperate Larix gmelinii forests in the Greater Khingan Mountains after forest fires provides a reference basis for the revegetation and reconstruction of fire sites.

The predictive power of phylogeny on growth rates in soil bacterial communities

Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.

Water availability creates global thresholds in multidimensional soil biodiversity and functions

Soils support an immense portion of Earth's biodiversity and maintain multiple ecosystem functions which are essential for human well-being. Environmental thresholds are known to govern global vegetation patterns, but it is still unknown whether they can be used to predict the distribution of soil organisms and functions across global biomes. Using a global field survey of 383 sites across contrasting climatic and vegetation conditions, here we showed that soil biodiversity and functions exhibited pervasive nonlinear patterns worldwide and are mainly governed by water availability (precipitation and potential evapotranspiration). Changes in water availability resulted in drastic shifts in soil biodiversity (bacteria, fungi, protists and invertebrates) and soil functions including plant-microbe interactions, plant productivity, soil biogeochemical cycles and soil carbon sequestration. Our findings highlight that crossing specific water availability thresholds can have critical consequences for the provision of essential ecosystem services needed to sustain our planet.

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO₂ emission at both temperatures, and phages played a role in maintaining Q₁₀ within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased V_angle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

Root-Soil Interactions for Pepper Accessions Grown under Organic and Conventional Farming

Modern agriculture has boosted the production of food based on the use of pesticides and fertilizers and improved plant varieties. However, the impact of some such technologies is high and not sustainable in the long term. Although the importance of rhizospheres in final plant performance, nutrient cycling, and ecosystems is well recognized, there is still a lack of information on the interactions of their main players. In this paper, four accessions of pepper are studied at the rhizosphere and root level under two farming systems: organic and conventional. Variations in soil traits, such as induced respiration, enzymatic activities, microbial counts, and metabolism of nitrogen at the rhizosphere and bulk soil, as well as measures of root morphology and plant production, are presented. The results showed differences for the evaluated traits between organic and conventional management, both at the rhizosphere and bulk soil levels. Organic farming showed higher microbial counts, enzymatic activities, and nitrogen mobilization. Our results also showed how some genotypes, such as Serrano or Piquillo, modified the properties of the rhizospheres in a very genotype-dependent way. This specificity of the soil-plant interaction should be considered for future breeding programs for soil-tailored agriculture.

Enhanced carbon emission driven by the interaction between functional microbial community and hydrocarbons: An enlightenment for carbon cycle

Soil microbial communities are usually regarded as one of the key players in the global element cycling. Moreover, an important consequence of oil contamination altering the structure of microbial communities is likely to result in an increased carbon emission. However, understanding of the complex interactions between environmental factors and biological communities is clearly lagging behind. Here it showed that the flux of carbon emissions increased in oil-contaminated soils, up to 13.64 g C·(kg soil)^-1·h^-1. This phenomenon was mainly driven by the enrichment of rare degrading microorganisms (e.g., Methylosinus, Marinobacter, Pseudomonas, Alcanivorax, Yeosuana, Halomonas and Microbulbifer) in the aerobic layer, rather than the anaerobic layer, which is more conducive to methane formation. In addition, petroleum hydrocarbons and environmental factors are equally important in shaping the structure of microbial communities (the ecological stability) and functional traits (e.g., fatty acid metabolism, lipid metabolism and amino acid metabolism) due to the different ecological sensitivities of microorganisms. Thus, it can be believed that the variability of rare hydrocarbon degrading microorganisms is of greater concern than changes in dominant microorganisms in oil-contaminated soil. Undoubtedly, this study could reveal the unique characterization of bacterial communities that mediate carbon emission and provide evidence for understanding the conversion from carbon stores to carbon gas release in oil-contaminated soils.

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.

Temperature fluctuation promotes the thermal adaptation of soil microbial respiration

The magnitude of the feedback between soil microbial respiration and increased mean temperature may decrease (a process called thermal adaptation) or increase over time, and accurately representing this feedback in models improves predictions of soil carbon loss rates. However, climate change entails changes not only in mean temperature but also in temperature fluctuation, and how this fluctuation regulates the thermal response of microbial respiration has never been systematically evaluated. By analysing subtropical forest soils from a 2,000 km transect across China, we showed that although a positive relationship between soil microbial biomass-specific respiration and temperature was observed under increased constant incubation temperature, an increasing temperature fluctuation had a stronger negative effect. Our results further indicated that changes in bacterial community composition and reduced activities of carbon degradation enzymes promoted the effect of temperature fluctuation. This adaptive response of soil microbial respiration suggests that climate warming may have a lesser exacerbating effect on atmospheric CO₂ concentrations than predicted.

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.

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.

Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming

Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature-growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (T_opt ) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0-30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in T_opt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.

Soil organic carbon decomposition responding to warming under nitrogen addition across Chinese vegetable soils

Chemical fertilization in excess and warming disrupt the soil microbes and alter resource stoichiometry, particularly in intensive vegetable soils, while the effects of these variables on the temperature sensitivity of soil organic carbon (SOC) decomposition (Q₁₀) and SOC stability remain elusive. Thus, we collected six long-term vegetable soils along a climatic gradient to examine the microbial mechanisms and resource stoichiometry effects on fluctuations in Q₁₀ and SOC stability induced by warming and fertilization from vegetable soils. Our results showed that the SOC decomposition was dominated by microbes and regulated by stoichiometry. Compared to cold sites, higher Q₁₀ of SOC decomposition was observed in warm sites, accompanied by lower enzyme activities, microbial CUE, and C:N ratio. In this context, warming reduced SOC stability as evidenced by up to 31.8% greater Q₁₀ (1.45) at warm sites than at cold sites (1.10) owing to less richness of microbial communities and lower microbial CUE. The relatively lower pH and labile organic C value restricted the development of microbial richness, and decreased C- and N-related enzyme activities and a lower C:N ratio resulted in microbial CUE reduction. Additionally, N fertilization altered the C:N imbalance and enhanced SOC stability in vegetable soils, exhibiting an increase of Q₁₀ values, particularly of great importance in warm sites. Collectively, our findings emphasize the importance of the microbial mechanism and resource stoichiometry in predicting variations in Q₁₀ and fluctuations in SOC stability, and provide theoretical advice on improving management policies in the context of warming and fertilization from vegetable soils.

Thermal adaptation occurs in the respiration and growth of widely distributed bacteria

Soil microbial respiration is an important factor in regulating carbon (C) exchange between the soil and atmosphere. Thermal adaptation of soil microorganisms will lead to a weakening of the positive feedback between climate warming and soil respiration. The thermal adaptation of microbial communities and fungal species has been proven. However, studies on the thermal adaptation of bacterial species, the most important decomposers in the soil, are still lacking. Here, we isolated six species of widely distributed dominant bacteria and studied the effects of constant warming and temperature fluctuations on those species. The results showed that constant warming caused a downregulation of respiratory temperature sensitivity (Q₁₀ ) of the bacterial species, accompanied by an elevation of the minimum temperature (T_min ) required for growth. Similar results were seen with the addition of temperature fluctuations, suggesting that both scenarios caused a significant thermal adaptation among the bacterial species. Fluctuating and increasing temperatures are considered an important component of future warming. Therefore, the inclusion of physiological responses of bacteria to these changes is essential to understand relationships between microbiota and temperature and enhance the prediction of global soil-atmosphere C feedbacks.

Mechanisms of soil organic carbon stability and its response to no-till: A global synthesis and perspective

Mechanisms of soil organic carbon (SOC) stabilization have been widely studied due to their relevance in the global carbon cycle. No-till (NT) has been frequently adopted to sequester SOC; however, limited information is available regarding whether sequestered SOC will be stabilized for long term. Thus, we reviewed the mechanisms affecting SOC stability in NT systems, including the priming effects (PE), molecular structure of SOC, aggregate protection, association with soil minerals, microbial properties, and environmental effects. Although a more steady-state molecular structure of SOC is observed in NT compared with conventional tillage (CT), SOC stability may depend more on physical and chemical protection. On average, NT improves macro-aggregation by 32.7%, and lowers SOC mineralization in macro-aggregates compared with CT. Chemical protection is also important due to the direct adsorption of organic molecules and the enhancement of aggregation by soil minerals. Higher microbial activity in NT could also produce binding agents to promote aggregation and the formation of metal-oxidant organic complexes. Thus, microbial residues could be stabilized in soils over the long term through their attachment to mineral surfaces and entrapment of aggregates under NT. On average, NT reduces SOC mineralization by 18.8% and PE intensities after fresh carbon inputs by 21.0% compared with CT (p < .05). Although higher temperature sensitivity (Q₁₀ ) is observed in NT due to greater Q₁₀ in macro-aggregates, an increase of soil moisture regime in NT could potentially constrain the improvement of Q₁₀ . This review improves process-based understanding of the physical and chemical mechanism of protection that can act, independently or interactively, to enhance SOC preservation. It is concluded that SOC sequestered in NT systems is likely to be stabilized over the long term.

Linking soil carbon availability, microbial community composition and enzyme activities to organic carbon mineralization of a bamboo forest soil amended with pyrogenic and fresh organic matter

Despite fresh and pyrogenic organic matter have been widely used as amendments to improve soil organic carbon (SOC) storage, mineralization that links to C quality and soil temperature, microbial community composition and enzyme activity remain poorly understood. This study aims to explore the effects of amendments (bamboo leaves and its biochar) and incubation temperature on mineralization, and disentangle the relationships of SOC mineralization with chemical composition of SOC, labile organic C, microbial community composition, and activities of enzymes in a subtropical bamboo forest soil. Results showed that cumulative soil CO₂ emissions ranked as bamboo leaf (Leaf) > bamboo leaf biochar (Biochar) > Control, regardless of the incubation temperature. Compared to the control, the Leaf treatment markedly increased, whereas the Biochar treatment decreased, the temperature sensitivity of SOC mineralization (P < 0.05). The cumulative soil CO₂ emission was positively correlated (P < 0.05) with water-soluble organic C (WSOC), microbial biomass C (MBC), O-alkyl C and alkyl C contents, and activities of β-glucosidase and dehydrogenase, but negatively correlated (P < 0.01) with aromatic C content, regardless of the incubation temperature. This indicated that the lower SOC mineralization rate and lower temperature sensitivity in the Biochar (cf. Leaf) treatment were intimately associated with the lower WSOC, MBC, O-alkyl C content, and β-glucosidase and dehydrogenase activities, and higher aromatic C content in the Biochar. The high relative abundance of bacteria relating SOC mineralization included Rhizobiales, Sphingobacteriales and JG30-KF-AS9, whereas that of fungi included Eurotiales, Sordariales, Agaricales and Helotiales. Our results revealed that the application of pyrogenic organic matter, as compared to the application of fresh organic matter, can reduce SOC mineralization and its temperature sensitivity in a subtropical forest soil by limiting the availability of C and microbial activity, and thus has a great potential for maintaining soil carbon stock in subtropical forest ecosystems.

Toward a function-first framework to make soil microbial ecology predictive

Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions. We first view the microbial community associated with a specific function as a whole and describe the dependence of microbial functions on environmental factors (e.g., the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of "biomarker" taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition. In this paper, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH, and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.

Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.