Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling

Cooling has stimulated soil carbon storage in forest ecosystems

The interactive effect of soil cooling and nitrogen (N) addition can accurately simulate climatic and anthropogenic effects on terrestrial and other land-based ecosystems, but direct empirical measurements on the effects of cooling and N addition on soil carbon (C) and N are lacking. Hence, transplanting soils into colder regions was used to evaluate the effects of cooling and N addition on soil C and N. We used PVCs of 30 cm in height and 8 cm in diameter to extract soil samples. Soil C and N were significantly (P < 0.05) increased by transplanting soils into colder regions. In contrast, cooling has insignificantly (P > 0.05) increased the soil dissolved organic C (DOC) and dissolved organic (DON), but the effect was negatively significant on soil pH compared to the C/N ratio. Similarly, N addition significantly increased the measured soil N stock. However, the effect was negatively significant on soil pH (P < 0.05) compared to the C/N ratio (P > 0.05). Nevertheless, the interaction of cooling and N addition did not affect the soil C and N storage. A similar effect was observed on the soil DOC and DON. The results presented here illustrate that transplanting soils into colder regions and N deposition has perfectly simulated the effects of climate-forcing factors on soil C and N storage in terrestrial and other land-based ecosystems. Accordingly, this study suggests that low temperatures have stimulated the accumulation of the measured soil organic and dissolved properties, but the effect is less consequential when low temperature interacts with N addition in high-elevation areas where ecosystem structures and functions are limited by temperature and may serve as a baseline for future research on land feedbacks to the climate system.

Unknown bacterial species lead to soil CO2 emission reduction by promoting lactic fermentation in alpine meadow on the Qinghai-Tibetan Plateau

Highly variable soil microbial respiration among grasslands has been identified as a major cause of uncertainty in regional carbon (C) budget estimation in the Qinghai-Tibetan Plateau; microbial metabolism mechanisms might explain this variation, but remain elusive. Therefore, we investigated soil CO2 production in incubated soils and detected the associated functional genes at four sampling sites from two major alpine grasslands on the Qinghai-Tibetan Plateau. The results showed that the cumulative CO2 emissions from alpine meadow soils were 71 %-83 % lower than those from alpine steppe soils. Both the enriched genes abundance encoding fermentation and glycolysis (Embden-Meyerhof pathway (EMP)) and the diminished genes encoding tricarboxylic acid cycle (TCA) and phosphate pentose pathway (PPP) explained the CO2 emission reduction in the alpine meadow soils. The EMP: PPP and fermentation: TCA cycle ratios in alpine meadow soils were 1.45- and 1.50-fold higher than those in alpine steppe soils, respectively. Such shifts in metabolic pathways were primarily caused by the increasing dominance of an unknown species of Desulfobacteraceae with high glycolytic potential, carrying a higher abundance of ldh genes during fermentation. These unknown species were promoted by warmer temperatures and higher precipitation in the alpine meadows. Further studies on the unknown species would enhance our understanding and predictability of C cycling in alpine grasslands.

Elevational changes in the bacterial community composition and potential functions in a Tibetan grassland

In the Tibetan grasslands, the distribution patterns of the microbial community structure and function along elevation gradients have attracted considerable attention due to the wide distribution of mountain slopes, but the controlling factors of these patterns are still unclear. Here we investigated the taxonomy and potential functions of soil bacteria along an elevation gradient in a Tibetan mountainous grassland in 2 years, aiming to explore the elevation patterns of the bacterial structure and function and the underlying drivers. High-throughput sequencing and environment attribute measurements were conducted to survey the bacterial and environment characters. Furthermore, PICRUSt2 for prediction of bacterial functions, iCAMP for unraveling the drivers controlling community assembly, and HMSC for variance partitioning of bacterial community composition were used. Elevation did not significantly affect the bacterial diversity but changed their composition, driven by both deterministic and stochastic processes. In addition, elevation did not significantly affect the relative importance of deterministic and stochastic processes. Soil carbon, nitrogen, and temperature were important deterministic factors in driving bacterial community structure. The genus Solirubrobacter in Actinobacteriota was identified as most elevation discriminatory. Based on these observations, the bacterial community in the Tibetan mountainous grasslands was more controlled by edaphic factors than temperature, indicating their relative stability under climate change scenarios.

Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition

Global warming is likely to affect the underground microbial communities in various ecosystems, but the response of soil microbial communities along a vertical depth profile to global warming has been elusive. Herein, we leveraged a warming field experiment in Qinghai-Tibet Plateau grassland and investigated the community structure of prokaryotes and fungi from the upper (0-15 cm) and lower (15-30 cm) strata under ambient and elevated temperature treatments. Three-years continual warming only significantly shifted the prokaryotic community within the upper strata and there was no significant effect observed for the fungal community. Additionally, under ambient temperature, there were significant differences between the two strata in both the prokaryotic and fungal communities, but under warming, this effect was alleviated. Next, the prokaryotic and fungal community assembly processes were measured by a phylogenetic-bin-based null approach (iCAMP). Though deterministic and stochastic processes dominated the assembly of prokaryotic and fungal communities, respectively, the deterministic processes were strengthened under warming for both communities. Specifically, the increased portion of homogeneous selection, contributing to a homogenous state, led to a smaller difference between prokaryotic communities of the two soil strata under warming. The smaller difference in the stochastic process component, i.e., dispersal limitation, contributed to the similar fungal community structures between the two strata under warming. This study deepens our understanding of warming effects on grassland microbial communities and gives greater insights on the underlying mechanisms for microbial assembly between upper and lower soil strata under warming scenarios.

Conversion effects of farmland to Zanthoxylum bungeanum plantations on soil organic carbon mineralization in the arid valley of the upper reaches of Yangtze River, China

Farmland conversion to forest is considered to be one of the effective measures to mitigate climate change. However, the impact of farmland conversion to forest land or grassland on soil CO₂ emission in arid areas is unclear due to the lack of comparative information on soil organic carbon (SOC) mineralization of different conversion types. The SOC mineralization in 0–100 cm soil layer in farmland (FL), abandoned land (AL) and different ages (including 8, 15, 20 and 28 years) of Zanthoxylum bungeanum plantations were measured by laboratory incubation. The size and decomposition rate of fast pool (C_f) and slow pool (C_s) in different land-use types and soil layers were estimated by double exponential model. The results showed that: 1) Farmland conversion increased the cumulative CO₂-C release (C_min) and SOC mineralization efficiency, and those indexes in AL were higher than that in Z. bungeanum plantations. The C_min and SOC mineralization efficiency of 0–100 cm soil increased with the ages of Z. bungeanum plantation. Both C_min and SOC mineralization efficiency decreased with the increase of soil depth; 2) Both soil C_f and C_s increased after farmland converted to Z. bungeanum plantations and AL. The C_s in the same soil layer increased with the ages of Z. bungeanum plantation, and the C_f showed a “V” type with the increased ages of Z. bungeanum plantation. The C_f and C_s decreased with the increase of soil depth in all land-use types; 3) Farmland conversion increased the decomposition rate of C_f (k₁) in all soil layer by 0.008–0.143 d⁻¹ and 0.082–0.148 d⁻¹ in Z. bungeanum plantations and AL, respectively. The k₁ was obviously higher in the 0−20 cm soil layer than that in other soil layers, while the decomposition rate of C_s (k₂) was not affected by FL conversion and soil depth; and 4) The initial soil chemical properties and enzyme activity affected SOC mineralization, especially the concentrations of total organic nitrogen (TON), SOC, easily oxidizable organic carbon (EOC) and microbial biomass carbon (MBC). It indicated that the conversion of farmland to Z. bungeanum plantations and AL increases SOC mineralization, especially in deeper soils, and it increased with the ages. The conversion of farmland to Z. bungeanum plantation is the optimal measure when the potential C sequestration of plant-soil system were taken in consideration.

Warming has a minor effect on surface soil organic carbon in alpine meadow ecosystems on the Qinghai-Tibetan Plateau

The alpine meadow ecosystem on the Qinghai-Tibetan Plateau (QTP) is very sensitive to warming and plays a key role in regulating global carbon (C) cycling. However, how warming affects the soil organic carbon (SOC) pool and related C inputs and outputs in alpine meadow ecosystems on the QTP remains unclear. Here, we combined two field experiments and a meta-analysis on field experiments to synthesize the responses of the SOC pool and related C cycling processes to warming in alpine meadow ecosystems on the QTP. We found that the SOC content of surface soil (0-10 cm) showed a minor response to warming, but plant respiration was accelerated by warming. In addition, the warming effect on SOC was not correlated with experimental and environmental variables, such as the method, magnitude and duration of warming, initial SOC content, mean annual temperature, and mean annual precipitation. We conclude that the surface SOC content is resistant to climate warming in alpine meadow ecosystems on the QTP.

Patterns of microbial arsenic detoxification genes in low-arsenic continental paddy soils

Microbes mediate the arsenic detoxification in paddy soils, determining the fate of arsenic in soils and its availability to rice plants, yet little is known about the structures and abundances of functional genes as well as the driving forces in low-arsenic paddy fields. To depict the arsenic detoxification functional gene patterns, 429 soil samples were collected from 39 paddy fields across four climatic zones in China, with the arsenic contents ranged from 9.76 to 19.74 mg kg^-1. GeoChip, a microarray-based metagenomic technique, was used to analyze the functional genes involved in arsenic detoxification. A total of three arsenic detoxification gene families were detected, aoxB, arxA (arsenite oxidase), and arsM (methyltransferase). Both the diversity and abundance of functional genes varied significantly among sampling sites (p < 0.05) and decreased along the arsenic gradient. Arsenic detoxification genes were carried by bacteria, archaea, and eukaryotes. Redundancy analysis showed that soil samples were grouped according to both climatic zones they located in and arsenic gradients at the continental scale. Soil pH, average annual temperature (AAT), arsenic, annual average precipitation (AAP), and CEC were the most important factors in shaping the functional structure. Structural equation modeling showed that AAT (r = 0.21), pH (r = -0.20), and arsenic contents (r = -0.11) directly affected the arsenic detoxification gene abundances. These findings provide an overall picture of microbial communities involved in arsenic detoxification in paddy soils and reveal the importance of climatic factors in shaping functional genes across a large spatial scale.

Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition

Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.

Climate mediates continental scale patterns of stream microbial functional diversity

BACKGROUND

Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China.

RESULTS

We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively.

CONCLUSIONS

We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change. Video Abstract.

Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance

Although biotic interactions among members of microbial communities have been conceived to be crucial for community assembly, it remains unclear how changes in environmental conditions affect microbial interaction and consequently system performance. Here, we adopted a random matrix theory-based network analysis to explore microbial interactions in triplicate anaerobic digestion (AD) systems, which is widely applied for organic pollutant treatments. The digesters were operated with incremental organic loading rates (OLRs) from 1.0 g volatile solids (VS)/liter/day to 1.3 g VS/liter/day and then to 1.5 g VS/liter/day, which increased VS removal and methane production proportionally. Higher resource availability led to networks with higher connectivity and shorter harmonic geodesic distance, suggestive of more intense microbial interactions and quicker responses to environmental changes. Strikingly, a number of topological properties of microbial network showed significant (P < 0.05) correlation with AD performance (i.e., methane production, biogas production, and VS removal). When controlling for environmental parameters (e.g., total ammonia, pH, and the VS load), node connectivity, especially that of the methanogenic archaeal network, still correlated with AD performance. Last, we identified the Methanothermus, Methanobacterium, Chlorobium, and Haloarcula taxa and an unclassified Thaumarchaeota taxon as keystone nodes of the network.IMPORTANCE AD is a biological process widely used for effective waste treatment throughout the world. Biotic interactions among microbes are critical to the assembly and functioning of the microbial community, but the response of microbial interactions to environmental changes and their influence on AD performance are still poorly understood. Using well-replicated time series data of 16S rRNA gene amplicons and functional gene arrays, we constructed random matrix theory-based association networks to characterize potential microbial interactions with incremental OLRs. We demonstrated striking linkage between network topological features of methanogenic archaea and AD functioning independent of environmental parameters. As the intricate balance of multiple microbial functional groups is responsible for methane production, our results suggest that microbial interaction may be an important, previously unrecognized mechanism in determining AD performance.

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient

Serving as “natural laboratories”, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600–3,400 m a.s.l.). The research area of this study was Mount (Mt.) “Schrankogel” in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000–3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.

Hierarchical drivers of soil microbial community structure variability in "Monte Perdido" Massif (Central Pyrenees)

Microbial activity is highly dependent on climatic factors (moisture and temperature) and edaphic characteristics in temperate ecosystems. Moreover, soil microbial community composition in high mountain areas is less known when compared to plant communities. In this study we investigated the soil microbial community from a functional perspective using PLFA (phospholipid fatty acid) methods in the four aspects of four summits (2,242 – 3,012 m above sea level) in the Spanish Central Pyrenees. Soil organic carbon (C), microbial biomass and nutrient dynamics (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{H}_{4}^{+}$$\end{document}NH4+ + \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{O}_{3}^{-}$$\end{document}NO3−, N mineralization and nitrification potential) were also determined. Microbial biomass C was highest in the lowermost summit and decreased by approximately 50, 14 and 12% with increasing altitude. In each summit soil \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{H}_{4}^{+}$$\end{document}NH4+ and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$N{O}_{3}^{-}$$\end{document}NO3− concentrations differed significantly among summits and aspects. Soil nitrification potential varied significantly between the factors summit and aspects, e.g., southerly vs. northerly, easterly vs. westerly aspects. Gram negative bacteria and Actinobacteria functional groups dominated the microbial community, with almost 40% of the total PLFA. Non-metric multidimensional scale (NMS) analysis showed that most of the PLFA functional groups were present in all summits and aspects, although with specific biomarkers. A high abundance of biomarkers 16:1ω9c and 16:0 2OH (gram negative bacteria) were obtained in the lowermost summit, while the biomarkers 16.1ω7cDMA (anaerobes) and 19:3ω6c (Eukaryote) were only found in the uppermost summit. Linear mixed model (lmm) analysis was used with summit as fixed effect and aspect as random effect. In general, our results demonstrate a fundamental role for environment, principally moisture, temperature and organic matter in explaining the pattern observed for soil PLFA biomarkers. Under a global change scenario, we need to shed light on the relationships between soil microbial functional groups and soil nutrient-related variables in order to identify the associated patterns of decomposition rates and soil processes driven by microbial communities in mountain areas. The results could thus be used in global predictive models on climate change impact on C or N cycles in these environments.

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.