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

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.