Microbial community dynamics alleviate stoichiometric constraints during litter decay

Seabuckthorn (Hippophae rhamnoides L.) plantation degradation aggravates microbial metabolic C and P limitations on the Northern Loess Plateau in China

Vegetation degradation in arid and semi-arid regions reduces plant C inputs to the soil, which can impede soil nutrient cycling because of the limited C source for microbial metabolism. However, whether vegetation degradation aggravates microbial nutrient limitation in degraded ecosystems in arid and semi-arid regions is not fully understood. Here, we investigated changes in soil enzyme activity and microbial nutrient limitation along a well-documented gradient of degraded seabuckthorn (Hippophae rhamnoides L.) (slightly degraded, canopy dieback <25 %, moderately degraded, canopy dieback 25 %-75 %, and severely degraded, canopy dieback >75 %) in Liang (long ridge) and gully channel locations in the Pisha Sandstone region of the Loess Plateau, China. We found that as the magnitude of seabuckthorn degradation increased, activities of C-acquiring enzymes and ratios of C:N and C:P enzymes (0.54-0.80 and 0.52-0.77, respectively) increased whereas the N:P enzyme ratio (0.93-0.99) decreased. Stoichiometric modelling further indicated that microorganisms were limited by soil C and P (vector angle >45°) in the seabuckthorn plantation region, and the degradation of seabuckthorn plantation aggravated microbial C and P limitations. Partial least squares path modelling revealed that seabuckthorn degradation (canopy dieback) was the main factor explaining microbial C limitation variations, while soil physicochemical properties (pH and soil moisture content) and understory plant parameters (litter biomass) were the major factors underlying microbial P limitation of long ridge and gully channel formations, respectively. Our findings highlight synergistic changes between aboveground and belowground processes, suggesting an unexpected negative effect of vegetation degradation on soil microbial community and nutrient cycling. These insights offer a direction for the development of plantation nutrients management strategies in semi-arid and arid areas.

Bacteria face trade-offs in the decomposition of complex biopolymers

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.

Microbial life-history strategies and particulate organic carbon mediate formation of microbial necromass carbon and stabilization in response to biochar addition

Microbial necromass carbon (MNC) contributes significantly to the formation of soil organic carbon (SOC). However, the microbial carbon sequestration effect of biochar is often underestimated and influenced by nutrient availability. The mechanisms associated with the formation and stabilization of MNC remain unclear, especially under the combined application of biochar and nitrogen (N) fertilizer. Thus, in a long-term field experiment (11 years) based on biochar application, we utilized bacterial 16S rRNA gene sequencing, fungal ITS amplicon sequencing, metagenomics, and microbial biomarkers to examine the interactions between MNC accumulation and microbial metabolic strategies under combined treatment with biochar and N fertilizer. We aimed to identify the critical microbial modules and species involved, and to analyze the sites where MNC was immobilized from various components. Biochar application increased the MNC content by 13.9 %. Among the MNC components, fungal necromass contributed more to MNC, but bacteria were more readily enriched after biochar application. The microbial life-history strategies that affected MNC formation under the application of various amounts biochar were linked to the N application level. Under N added at 226.5 kg ha-1, communities such as Actinobacteria and Bacteroidetes with high-growth yield strategies were prevalent and contributed to MNC production. By contrast, under N added at 113.25 kg ha-1 with high biochar application, Proteobacteria with strong resource acquisition strategies were dominant and MNC accumulation was lower. The mineral-associated organic carbon pool was rapidly saturated with the addition of biochar, so the contribution of fungal necromass carbon may have been reduced by reutilization, thereby resulting in the more rapid preservation of bacterial necromass carbon in the particulate organic carbon pool. Overall, our findings indicate that microbial life history traits are crucial for linking microbial metabolic processes to the accumulation and stabilization of MNC, thereby highlighting the their importance for SOC accumulation in farmland soils, and the need to tailor appropriate biochar and N fertilizer application strategies for agricultural soils.

Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem

Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.

The size and diversity of microbes determine carbon use efficiency in soil

Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China

Dynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p > 0.05) and the fungal diversity of Shannon-Wiener index even decreased (p ≤ 0.05). The abundances of microbial carbohydrate degradation functional genes of cellulase, hemicellulase, and pectinase also increased with forest succession (p ≤ 0.05 for all). However, the chitinase gene abundance did not change with forest succession (p > 0.05) and the amylase gene abundance decreased firstly in middle-succession forest and then increased in late-succession forest. Further analysis indicated that changes of functional gene abundance in cellulase, hemicellulase, and pectinase were primarily affected by soil organic carbon, soil total nitrogen, and soil moisture, whereas the variation of amylase gene abundance was well explained by soil phosphorus and litterfall. Overall, we created a metagenome profile of soil microbes in subtropical forest succession and fostered our understanding of microbially-mediated soil carbon cycling.

Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism

Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.

Deciphering Biotic and Abiotic Mechanisms Underlying Straw Decomposition and Soil Organic Carbon Priming in Agriculture Soils Receiving Long-Term Fertilizers

Straw-related carbon (C) dynamics are central for C accrual in agro-ecosystems and should be assessed by investigating their decomposition and soil organic carbon (SOC) priming effects. Our understanding of biotic and abiotic mechanisms underpinning these two C processes, however, is still not sufficiently profound. Soils that had received organic and mineral fertilizers for 26 years were sampled for a 28 day incubation experiment to assess 13C-labeled straw decomposition and SOC priming effects. On the basis of analyzing physicochemical properties, fungal taxonomic (MiSeq sequencing) and functional (metagenomics) guilds, we quantified the contributions of biotic and abiotic attributes to straw decomposition and SOC priming. Here, we propose two distinct mechanisms underlying straw decomposition and SOC priming in agriculture soils: (i) accelerated straw mineralization in manure-treated soils was mainly driven by biotic forces, while (ii) larger SOC priming in NPK-amended soils was through abiotic regulation.

Biochar-Associated Free Radicals Reduce Soil Bacterial Diversity: New Insight into Ecoenzymatic Stoichiometry

The toxicity of environmentally persistent free radicals (EPFRs), often generated during biochar production, on soil bacteria is still not truly reflected when considering the conditions in real soil. Herein, the influence of free radicals within biochar on soil bacteria was investigated from the perspectives of enzyme activity, community structure, and ecoenzymatic stoichiometry. Biochar addition enhanced the contents of EPFRs and derived hydroxyl radicals (•OH) in the soil, while it reduced bacterial alpha diversity by 5.06-35.44%. The results of redundancy analysis and inhibition experiments collectively demonstrated the key role of EPFRs and •OH in reducing the bacterial alpha diversity. Specifically, EPFRs and •OH increased the stoichiometric imbalance by promoting the release of dissolved organic carbon and ammonium N, thus aggravating the P limitation in soil. This was further confirmed by increased alkaline phosphatase activity from 702 to 874 nmol g-1 h-1. The P limitation induced by EPFRs and •OH decreased the bacterial alpha diversity, as evidenced by the negative correlation between P limitation and bacterial alpha diversity (r2 = -0.931 to -0.979, P < 0.01) and the structural equation model. The obtained results demonstrate a ubiquitous but previously overlooked mechanism for bacterial toxicity of biochar-associated free radicals, providing scientific guidance for safe utilization of biochar.

Fungal necromass is reduced by intensive drought in subsoil but not in topsoil

The frequency and intensity of droughts worldwide are challenging the conservation of soil organic carbon (SOC) pool. Microbial necromass is a key component of SOC, but how it responds to drought at specific soil depths remains largely unknown. Here, we conducted a 3-year field experiment in a forest plantation to investigate the impacts of drought intensities under three treatments (ambient control [CK], moderate drought [30% throughfall removal], and intensive drought [50% throughfall removal]) on soil microbial necromass pools (i.e., bacterial necromass carbon, fungal necromass carbon, and total microbial necromass carbon). We showed that the effects of drought on microbial necromass depended on microbial groups, soil depth, and drought intensity. While moderate drought increased total (+9.1% ± 3.3%) and fungal (+13.5% ± 4.9%) necromass carbon in the topsoil layer (0-15 cm), intensive drought reduced total (-31.6% ± 3.7%) and fungal (-43.6% ± 4.0%) necromass in the subsoil layer (15-30 cm). In contrast, both drought treatments significantly increased the BNC in the topsoil and subsoil. Our results suggested that the effects of drought on the microbial necromass of the subsoil were more pronounced than those of the topsoil. This study highlights the complex responses of microbial necromass to drought events depending on microbial community structure, drought intensity and soil depth with global implications when forecasting carbon cycling under climate change.

C:N:P stoichiometry of plants, soils, and microorganisms: Response to altered precipitation

Precipitation changes modify C, N, and P cycles, which regulate the functions and structure of terrestrial ecosystems. Although altered precipitation affects above- and belowground C:N:P stoichiometry, considerable uncertainties remain regarding plant-microbial nutrient allocation strategies under increased (IPPT) and decreased (DPPT) precipitation. We meta-analyzed 827 observations from 235 field studies to investigate the effects of IPPT and DPPT on the C:N:P stoichiometry of plants, soils, and microorganisms. DPPT reduced leaf C:N ratio, but increased the leaf and root N:P ratios reflecting stronger decrease of P compared with N mobility in soil under drought. IPPT increased microbial biomass C (+13%), N (+15%), P (26%), and the C:N ratio, whereas DPPT decreased microbial biomass N (-12%) and the N:P ratio. The C:N and N:P ratios of plant leaves were more sensitive to medium DPPT than to IPPT because drought increased plant N content, particularly in humid areas. The responses of plant and soil C:N:P stoichiometry to altered precipitation did not fit the double asymmetry model with a positive asymmetry under IPPT and a negative asymmetry under extreme DPPT. Soil microorganisms were more sensitive to IPPT than to DPPT, but they were more sensitive to extreme DPPT than extreme IPPT, consistent with the double asymmetry model. Soil microorganisms maintained stoichiometric homeostasis, whereas N:P ratios of plants follow that of the soils under altered precipitation. In conclusion, specific N allocation strategies of plants and microbial communities as well as N and P availability in soil critically mediate C:N:P stoichiometry by altered precipitation that need to be considered by prediction of ecosystem functions and C cycling under future climate change scenarios.

Whole-soil-profile warming does not change microbial carbon use efficiency in surface and deep soils

The paucity of investigations of carbon (C) dynamics through the soil profile with warming makes it challenging to evaluate the terrestrial C feedback to climate change. Soil microbes are important engines driving terrestrial biogeochemical cycles; their carbon use efficiency (CUE), defined as the proportion of metabolized organic C allocated to microbial biomass, is a key regulator controlling the fate of soil C. It has been theorized that microbial CUE should decline with warming; however, empirical evidence for this response is scarce, and data from deeper soils are particularly scarce. Here, based on soil samples from a whole-soil-profile warming experiment (0 to 1 m, +4 °C) and 18O tracing approach, we examined the vertical variation of microbial CUE and its response to ~3.3-y experimental warming in an alpine grassland on the Qinghai-Tibetan Plateau. Microbial CUE decreased with soil depth, a trend that was primarily controlled by soil C availability. However, warming had limited effects on microbial CUE regardless of soil depth. Similarly, warming had no significant effect on soil C availability, as characterized by extractable organic C, enzyme-based lignocellulose index, and lignin phenol-based ratios of vanillyls, syringyls, and cinnamyls. Collectively, our work suggests that short-term warming does not alter microbial CUE in either surface or deep soils, and emphasizes the regulatory role of soil C availability on microbial CUE.

Precipitation Dominates the Allocation Strategy of Above- and Belowground Biomass in Plants on Macro Scales

The allocation of biomass reflects a plant's resource utilization strategy and is significantly influenced by climatic factors. However, it remains unclear how climate factors affect the aboveground and belowground biomass allocation patterns on macro scales. To address this, a study was conducted using aboveground and belowground biomass data for 486 species across 294 sites in China, investigating the effects of climate change on biomass allocation patterns. The results show that the proportion of belowground biomass in the total biomass (BGBP) or root-to-shoot ratio (R/S) in the northwest region of China is significantly higher than that in the southeast region. Significant differences (p < 0.05) were found in BGBP or R/S among different types of plants (trees, shrubs, and herbs plants), with values for herb plants being significantly higher than shrubs and tree species. On macro scales, precipitation and soil nutrient factors (i.e., soil nitrogen and phosphorus content) are positively correlated with BGBP or R/S, while temperature and functional traits are negatively correlated. Climate factors contribute more to driving plant biomass allocation strategies than soil and functional trait factors. Climate factors determine BGBP by changing other functional traits of plants. However, climate factors influence R/S mainly by affecting the availability of soil nutrients. The results quantify the productivity and carbon sequestration capacity of terrestrial ecosystems and provide important theoretical guidance for the management of forests, shrubs, and herbaceous plants.

The Invasive Tradescantia zebrina Affects Litter Decomposition, but It Does Not Change the Lignocellulolytic Fungal Community in the Atlantic Forest, Brazil

Invasive plants affect ecosystems across various scales. In particular, they affect the quality and quantity of litter, which influences the composition of decomposing (lignocellulolytic) fungal communities. However, the relationship among the quality of invasive litter, lignocellulolytic cultivated fungal community composition, and litter decomposition rates under invasive conditions is still unknown. We evaluated whether the invasive herbaceous Tradescantia zebrina affects the litter decomposition in the Atlantic Forest and the lignocellulolytic cultivated fungal community composition. We placed litter bags with litter from the invader and native plants in invaded and non-invaded areas, as well as under controlled conditions. We evaluated the lignocellulolytic fungal communities by culture method and molecular identification. Litter from T. zebrina decomposed faster than litter from native species. However, the invasion of T. zebrina did not alter decomposition rates of either litter type. Although the lignocellulolytic fungal community composition changed over decomposition time, neither the invasion of T. zebrina nor litter type influenced lignocellulolytic fungal communities. We believe that the high plant richness in the Atlantic Forest enables a highly diversified and stable decomposing biota formed in conditions of high plant diversity. This diversified fungal community is capable of interacting with different litter types under different environmental conditions.

Buffering effect of global vegetation on the air-land exchange of mercury: Insights from a novel terrestrial mercury model based on CESM2-CLM5

The vegetation uptake of atmospheric elemental mercury [Hg(0)] and its subsequent littering are critical processes of the terrestrial Hg cycles. There is a large uncertainty in the estimated global fluxes of these processes due to the knowledge gap in the underlying mechanisms and their relationship with environmental factors. Here, we develop a new global model based on the Community Land Model Version 5 (CLM5-Hg) as an independent component of the Community Earth System Model 2 (CESM2). We explore the global pattern of gaseous elemental Hg [Hg(0)] uptake by vegetation and the spatial distribution of litter Hg concentration constrained by observed datasets as well as its driving mechanism. The annual vegetation uptake of Hg(0) is estimated as 3132 Mg yr^-1, which is considerably higher than previous global models. The scheme of dynamic plant growth including stomatal activities substantially improves the estimation for global terrestrial distribution of Hg, compared to the leaf area index (LAI) based scheme that is often used by previous models. We find the global distribution of litter Hg concentrations driven by vegetation uptake of atmospheric Hg(0), which are simulated to be higher in East Asia (87 ng/g) than in the Amazon region (63 ng/g). Meanwhile, as a significant source for litter Hg, the formation of structural litter (cellulose litter + lignin litter) results in a lagging effect between Hg(0) deposition and litter Hg concentration, implying the buffering effect of vegetation on the air-land exchange of Hg. This work highlights the importance of vegetation physiology and environmental factors in understanding the vegetation sequestration of atmospheric Hg globally, and calls for greater efforts to protect forests and afforestation.

Soil microbial community structure dynamics shape the rhizosphere priming effect patterns in the paddy soil

Microbial community structure plays a crucial part in soil organic carbon (SOC) decomposition and variation of rhizosphere priming effects (RPEs) during plant growth. However, it is still uncertain how bacterial community structure regulates RPEs in soil and how RPE patterns respond to plant growth. Therefore, we conducted an experiment to examine the RPE response to plant growth and nitrogen (N) addition (0 (N0), 150 (N150), and 300 (N300) kg N ha^-1) using the ¹³C natural abundance method in a C₃ soil (paddy soil) - C₄ plant (maize, Zea mays L.) system; we then explored the underlying biotic mechanisms using 16S rRNA sequencing techniques. Networks were constructed to identify keystone taxa and to analyze the correlations between network functional modules of bacterial community and C decomposition. The results indicated that negative and positive RPEs occurred on Day 30 and Day 75 after maize planting, respectively. Bacterial community structure significantly changed and tended to shift from r-strategists toward K-strategists with changing labile C: N stoichiometry and soil pH during plant growth stages. The different network modules of bacterial community were aggregated in response to RPE pattern variation. Caulobacteraceae, Bacillus, and Chitinophagaceae were keystone taxa on Day 30, while Gemmatimonas, Candidatus Koribacter, and Xanthobacteraceae were keystone taxa on Day 75. Moreover, keystone taxa with different C utilization strategies were significantly different between the two growth stages and related closely to different RPE patterns. This study provides deeper insights into the network structure of bacterial communities corresponding to RPE patterns and emphasizes the significance of keystone taxa in RPE variation.

Organic amendments with high proportion of heterocyclic compounds promote soil microbiome shift and microbial use efficiency of straw-C

Soil microbial use efficiency of straw carbon (C), which is the proportion of straw-C microbes assimilate into new biosynthetic material relative to C lost out of the system as CO₂, is critical in increasing soil organic C (SOC) content, and hence maintaining soil fertility and productivity. However, the effect of chemical structures of the organic amendments (OAs) on the microbial use efficiency of straw-C remains unclear. The effect of the chemical structure of the OAs on microbial use efficiency of straw-C was elucidated by a combination of ¹³C-straw labeling with high-throughput sequencing and pyrolysis-GC/MS. We found a strong positive correlation between the microbial use efficiency of straw-C and the proportion of heterocyclic compounds (Hete_C). The microbial use efficiency of straw-C was highest in soil supplemented with Hete_C-dominant OAs, which significantly shifted microbial community structure toward fungal dominance. Specifically, fungal-to-bacterial ratio, fungal richness, and the relative abundance of Ascomycota were higher in soil with a higher proportion of Hete_C-dominant OAs. Together, our study suggests that OAs with high proportion of Hete_C promote the microbial use efficiency of straw-C by increasing the dominance of fungi in the soil microbial community in agroecosystems.

Biotic Interactions in Soil are Underestimated Drivers of Microbial Carbon Use Efficiency

Microbial carbon use efficiency (CUE)-the balance between microbial growth and respiration-strongly impacts microbial mediated soil carbon storage and is sensitive to many well-studied abiotic environmental factors. However, surprisingly, little work has examined how biotic interactions in soil may impact CUE. Here, we review the theoretical and empirical lines of evidence exploring how biotic interactions affect CUE through the lens of life history strategies. Fundamentally, the CUE of a microbial population is constrained by population density and carrying capacity, which, when reached, causes species to grow more quickly and less efficiently. When microbes engage in interspecific competition, they accelerate growth rates to acquire limited resources and release secondary chemicals toxic to competitors. Such processes are not anabolic and thus constrain CUE. In turn, antagonists may activate one of a number of stress responses that also do not involve biomass production, potentially further reducing CUE. In contrast, facilitation can increase CUE by expanding species realized niches, mitigating environmental stress and reducing production costs of extracellular enzymes. Microbial interactions at higher trophic levels also influence CUE. For instance, predation on microbes can positively or negatively impact CUE by changing microbial density and the outcomes of interspecific competition. Finally, we discuss how plants select for more or less efficient microbes under different contexts. In short, this review demonstrates the potential for biotic interactions to be a strong regulator of microbial CUE and additionally provides a blueprint for future research to address key knowledge gaps of ecological and applied importance for carbon sequestration.

Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times

Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.

Distribution and dynamics of particulate organic matter in Indian mangroves during dry period

The distribution and possible sources of particulate organic carbon (POC) and particulate nitrogen (PN) in seven mangroves ecosystems along the east and west coast of India were examined, to understand their contribution to coastal biogeochemistry. Suspended particulate matter (SPM) concentration in mangrove waters were about ~ 1.6-fold higher in west coast (Gulf of Kachchh (GOK), Mandovi-Zuari (MA-ZU) and Karwar-Kumta (KR-KU)], whereas the mean POC content in SPM along east coast [Sundarbans (SUN), Bhitarkanika (BHK), Coringa (COR) and Pichavaram-Muthupet (PI-MU)] was nearly two times higher than the west coast (1.97 ± 0.91% and 1.06 ± 0.29%), respectively. The results indicated that the influence of the land-based contaminants on the water quality parameters (dissolved oxygen, pH, salinity, nutrients and chlorophyll-a, etc.), which primarily regulated the distribution and transformation of organic carbon in these mangrove waters. Among the studied systems, an extremely high DOC/POC ratio (5.72 ± 1.64) with low pH and DO in COR waters clearly indicated the labile nature of the organic matter influenced by anthropogenic stress. Strong correlation between POC and PN indicated a similar origin in particulate organic matter. The ratios of POC/PN and POC/Chl-a showed significant spatial variation ranging from 5.5 to 18.7 and 126 to 1057, respectively. The results indicated that significant fraction of in-situ primary production contributed to particulate organic matter (POM) pool in all Indian mangrove waters except the GOK and the SUN waters, where sediment resuspension and mangrove derived organic matter were the dominant POM sources.

Methanotrophy Alleviates Nitrogen Constraint of Carbon Turnover by Rice Root-Associated Microbiomes

The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N₂ fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N₂ fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of carbon and nitrogen in rice roots. ¹⁵N₂-stable isotope probing showed that N₂-fixing activity was stimulated 160-fold by CH₄ oxidation from 0.27 to 43.3 μmol N g^–1 dry weight root biomass, and approximately 42.5% of the fixed N existed in the form of ¹⁵N-NH₄⁺ through microbial mineralization. Nitrate amendment almost completely abolished N₂ fixation. Ecophysiology flux measurement indicated that methane oxidation-induced N₂ fixation contributed only 1.9% of total nitrogen, whereas methanotrophy-primed mineralization accounted for 21.7% of total nitrogen to facilitate root carbon turnover. DNA-based stable isotope probing further indicated that gammaproteobacterial Methylomonas-like methanotrophs dominated N₂ fixation in CH₄-consuming roots, whereas nitrate addition resulted in the shift of the active population to alphaproteobacterial Methylocystis-like methanotrophs. Co-occurring pattern analysis of active microbial community further suggested that a number of keystone taxa could have played a major role in nitrogen acquisition through root decomposition and N₂ fixation to facilitate nutrient cycling while maintaining soil productivity. This study thus highlights the importance of root-associated methanotrophs as both biofilters of greenhouse gas methane and microbial engines of bioavailable nitrogen for rice growth.

Linkages of nitrogen-cycling microbial resistance and resilience to soil nutrient stoichiometry under dry-rewetting cycles with different fertilizations and temperatures in a vegetable field

Multiple dry-rewetting (DRW) cycles occur in intensively managed vegetable fields due to frequent tillage and irrigation. Soil nitrogen (N) cycling depends on the resistance and resilience of related microbial populations to DRW cycles, which could be closely related to soil nutrient status. However, the linkage of N-cycling microbial resistance and resilience and soil nutrient stoichiometry remains unknown in vegetable field. Here, we established four fertilization treatments in a four-year greenhouse vegetable field: no N fertilization, synthesized N fertilization, substituting 50% of chemical N with organic fertilizer or biofertilizer. Then, we set up an 85-day DRW-cycling incubation at 15, 25 and 35 °C including a 55-day fluctuating moisture for microbial resistance and then a 30-day constant moisture for microbial resilience. The results showed that microbial resistance was high (resistance index = 0.87- 0.99) in response to DRW cycles, but microbial resilience was generally low (resilience index = -0.36- 0.76), especially in 50% organic substitution or 15 °C. N-cycling microbes showed an important trade-off between their resistance and resilience to DRW cycles. Furthermore, most treatments showed microbial carbon limitation and N abundance during DRW cycles and recovered gradually to the undisturbed state. Microbial resistance was significantly related to the soil nutrient stoichiometry of carbon, N and phosphorus, while microbial resilience was mainly correlated with carbon-related indicators. In conclusion, N-cycling microbes presented good stability with oligotrophic strategy to frequent DRW cycles, which was linked to not only the historical legacy effect of DRW cycles but also soil nutrient stoichiometry in the vegetable field.

Integrating McGill Wetland Model (MWM) with peat cohort tracking and microbial controls

Peatlands store a large amount of organic carbon and are vulnerable to climate change and human disturbances. However, ecosystem-scale peatland models often do not explicitly simulate the decrease in peat substrate quality, i.e., decomposability or the dynamics of decomposers during peat decomposition, which are key controls in determining peat carbon's response to a changing environment. In this paper, we incorporated the tracking of each year's litter input (a cohort) and controls of microbial processes into the McGill Wetland Model (MWMmic) to address this discrepancy. Three major modifications were made: (1) the simple acrotelm-catotelm decomposition model in MWM was changed into a time-aggregated cohort model, to track the decrease in peat quality with decomposition age; (2) microbial dynamics: growth, respiration and death were incorporated into the model and decomposition rates are regulated by microbial biomass; and (3) vertical and horizontal transport of the dissolved organic carbon (DOC) were added and used to regulate the growth of microbial biomass. MWMmic was evaluated against measurements from the Mer Bleue peatland, a raised ombrotrophic bog located in southern Ontario, Canada. The model was able to replicate microbial and DOC dynamics, while at the same time reproduce the ecosystem-level CO₂ and DOC fluxes. Sensitivity analysis with MWMmic showed increased peatland resilience to perturbations compared to the original MWM, because of the tracking of peat substrate quality. The analysis revealed the most important parameters in the model to be microbial carbon use efficiency (CUE) and turnover rate. Simulated microbial adaptation with those two physiological parameters less sensitive to disturbances leads to a significantly larger peat C loss in response to warming and water table drawdown. Thus, the rarely explored peatland microbial physiological traits merit further research. This work paves the way for further model development to examine important microbial controls on peatland's biogeochemical cycling.

Glucose addition promotes C fixation and bacteria diversity in C-poor soils, improves root morphology, and enhances key N metabolism in apple roots

The interaction between plant, soil and microorganism plays a crucial role in sustainable development of terrestrial ecosystem function and diversity. However, little information is known about how plant growth, soil organic carbon (C) fractions and microorganism respond to exogenous C addition in soils with low organic C content. Three levels of ¹³C-glucose (equal to 0, 100% and 500% of initial microbial biomass C) were added to non-sterilized (corresponding to treatment abbreviation of CK, Glu-1, Glu-2, respectively) and sterilized soils (corresponding to treatment abbreviation of SS, SS+Glu-1, SS+Glu-2, respectively) planted with apple rootstock (Malus baccata (L.) Borkh.) seedings. The objectives of this study were to analyse the dynamics of soil organic C (SOC) fractions and soil bacterial community diversity with glucose levels and soil sterilization, and to explore the morphology of roots and nitrogen (N) metabolism by plant after glucose addition to sterilized/non-sterilized soils. Results showed that the contents of labile organic C fractions were significantly varied (P<0.05) with the levels of glucose addition and soil sterilization. SS+Glu-2 and Glu-2 treatments increased the contents of labile organic C fractions, on average, by 48.47% and 35.33% compared with no glucose addition, respectively. About 21.42% and 16.17% of glucose-C remained in sterilized and non-sterilized soils, respectively at the end of experiment (day 45). Regardless of soil sterilized or not, the glucose addition increased the richness and diversity indices of soil bacterial community compared with no-glucose addition. The glucose addition optimized root zone conditions, and enhanced root vitality, morphology and biomass. Both SS+Glu-2 and Glu-2 treatments significantly enhanced (P<0.05) the contents of nitrate (NO₃^—N) and nitrite (NO₂^—N), but sharply decreased (P<0.05) the ammonium (NH₄⁺-N) content compared with no glucose addition. Also, these two treatments significantly (P<0.05) increased the enzymic activities and gene transcript levels involved in root N metabolism, which demonstrated that the high level of glucose addition promoted N assimilation and transformation into free amino acids by root. Overall, the addition of exogenous C to not only promotes its fixation and bacterial community diversity in C-poor soils, but also improves root morphology and N absorption by plant.

Soil nutrient variability mediates the effects of erosion on soil microbial communities: results from a modified topsoil removal method in an agricultural field in Yunnan plateau, China

Soil erosion can affect the nature and distribution of soil carbon and nutrients, directly and indirectly influencing microbially facilitated processes of mineralization, ammoniation, and nitrification, thus affecting soil nutrients cycling. However, little is known about how soil erosion affects soil microorganisms. Since 2012, we conducted a modified soil erosion simulation experiment of topsoil removal method in an agricultural field to simulate erosion depths of 5, 10, 20, 30, and 40 cm versus a control (0 cm). The results showed that Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, Actinobacteria, and Firmicutes were the dominant soil microbial (here: Bacteria and Archaea) phyla, and Acidothermus, Candidatus Solibacter, Acidibacter, Bryobacter, and Actinospica were the dominant genera in all samples. The relative abundance of Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Thaumarchaeota, Acidothermus, Candidatus Solibacter, Acidibacter, Bryobacter, Actinospica, and Rhodanobacter decreased with the increase of erosion depths, while Chloroflexi and Firmicutes increased with the increase of erosion depths. Soil microbial community structure was altered significantly at 30- and 40-cm soil erosion depth in comparison to control. Soil nutrient variability caused by soil erosion had a greater impact on soil microbial community composition than that of soil mechanical composition. Soil erosion indirectly affected microbial community composition through negative effects on soil available potassium, total phosphorus, total nitrogen, and sand content. We thus highlight the importance of soil nutrients monitoring in different soil erosion levels to make the proper ecological restoration strategies to improve soil environment which soil microorganisms depend on.

Contrasting effects of carbon source recalcitrance on soil phosphorus availability and communities of phosphorus solubilizing microorganisms

Carbon (C) additions to soil interact through chemical and microbiological processes to cause changes in soil phosphorus (P) availability. However, the response of soil P transformations and relevant microbial communities to C additions having different degrees of recalcitrance remains uncertain. We studied the effects of glucose, hemicellulose and lignin addition on soil P availability, P transformation processes and relevant microbial activity and communities in a P-deficient flooded soil. Lignin significantly increased soil available P concentrations, which was attributed to chemical release of inorganic P and increased alkaline phosphatase activity. Glucose and hemicellulose additions stimulated microbial metabolism of C thereby enhancing microbial demand for P, with increased soil P availability especially in the early incubation period. Glucose or hemicellulose addition changed soil microbial diversity and community composition, leading to enhanced growth and interactions of P solubilizing microorganisms such as Desulfitobacterium, Bacillus and Desulfosporosinus. Our results infer the importance of pH alteration and competitive sorption between PO₄ and functional groups of recalcitrant C (e.g., lignin) with Fe/Al (hydr) oxides in regulating soil P availability. Further, the microbial response to labile C additions led to increased P availability in the P-deficient soil. This study provides important mechanistic information to guide microbially-regulated soil P management in agricultural ecosystems.

Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review

Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem’s C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem’s C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to 0.8. Thermodynamics, ecological environmental factors, substrate nutrient quality and availability, stoichiometric balance, and microbial community composition all influence this variation. In the future, soil microbial CUE research should focus on quantitative analysis of trace metabolic components, analysis of the regulation mechanism of biological-environmental interactions, and optimization of the carbon cycle model of microorganisms’ dynamic physiological response process.

Forest conversion to plantations: A meta-analysis of consequences for soil and microbial properties and functions

Primary or secondary forests around the world are increasingly being converted into plantations. Soil microorganisms are critical for all biogeochemical processes in ecosystems, but the effects of forest conversion on microbial communities and their functioning remain unclear. Here, we conducted a meta-analysis to quantify the impacts that converting forests to plantations has on soil microbial communities and functioning as well as on the associated plant and soil properties. We collected 524 paired observations from 138 studies globally. We found that conversion leads to broad range of adverse impacts on soils and microorganisms, including on soil organic carbon (-24%), total nitrogen (-29%), bacterial and fungal biomass (-36% and -42%, respectively), microbial biomass carbon (MBC, -31%) and nitrogen (-33%), and fungi to bacteria ratio (F:B, -16%). In addition, we found impacts on the ratio of MBC to soil organic C (qMBC, -20%), microbial respiration (-18%), N mineralization (-18%), and enzyme activities including β-1,4-glucosidase (-54%), β-1,4-N-acetylglucosaminidase (-39%), and acid phosphatase (ACP; -34%). In contrast, conversion to plantations increases bacterial richness (+21%) and microbial metabolic quotient (qCO₂ , +21%). The effects of forest conversion were consistent across stand ages, stand types, and climate zone. Soil C and N contents as well as the C:N ratio were the main factors responsible for the changes of microbial C, F:B, and bacterial richness. The responses of qCO₂ , N mineralization, and ACP activity were mainly driven by the reductions in F:B, MBC, and soil C:N. Applying macro-ecology theory on ecosystem disturbance in soil microbial ecology, we show that microbial groups shifted from K to r strategists after conversion to plantations. Our meta-analysis underlines the adverse effects of natural forests conversion to plantations on soil microbial communities and functioning, and suggests that the preservation of soil functions should be a consideration in forest management practices.

Substrate control of sulphur utilisation and microbial stoichiometry in soil: Results of 13C, 15N, 14C, and 35S quad labelling

Global plant sulphur (S) deficiency is increasing because of a reduction in sulphate-based fertiliser application combined with continuous S withdrawal during harvest. Here, we applied ¹³C, ¹⁵N, ¹⁴C, and ³⁵S quad labelling of the S-containing amino acids cysteine (Cys) and methionine (Met) to understand S cycling and microbial S transformations in the soil. The soil microorganisms absorbed the applied Cys and Met within minutes and released SO₄^2- within hours. The SO₄^2- was reutilised by the MB within days. The initial microbial utilisation and SO₄^2- release were determined by amino acid structure. Met released 2.5-fold less SO₄^2- than Cys. The microbial biomass retained comparatively more C and S from Met than Cys. The microorganisms decomposed Cys to pyruvate and H₂S whereas they converted Met to α-ketobutyrate and S-CH₃. The microbial stoichiometries of C, N, and S derived from Cys and Met were balanced after 4 d by Cys-derived SO₄^2- uptake and Met-derived CO₂ release. The microbial C:N:S ratio dynamics showed rapid C utilisation and loss, stable N levels, and S accumulation. Thus, short-term organic S utilisation by soil microorganisms is determined by amino acid structure whilst long-term organic S utilisation by soil microorganisms is determined by microbially controlled stoichiometry.

Intracellular Storage Reduces Stoichiometric Imbalances in Soil Microbial Biomass – A Theoretical Exploration

Microbial intracellular storage is key to defining microbial resource use strategies and could contribute to carbon (C) and nutrient cycling. However, little attention has been devoted to the role of intracellular storage in soil processes, in particular from a theoretical perspective. Here we fill this gap by integrating intracellular storage dynamics into a microbially explicit soil C and nutrient cycling model. Two ecologically relevant modes of storage are considered: reserve storage, in which elements are routed to a storage compartment in proportion to their uptake rate, and surplus storage, in which elements in excess of microbial stoichiometric requirements are stored and limiting elements are remobilized from storage to fuel growth and microbial maintenance. Our aim is to explore with this model how these different storage modes affect the retention of C and nutrients in active microbial biomass under idealized conditions mimicking a substrate pulse experiment. As a case study, we describe C and phosphorus (P) dynamics using literature data to estimate model parameters. Both storage modes enhance the retention of elements in microbial biomass, but the surplus storage mode is more effective to selectively store or remobilize C and nutrients according to microbial needs. Enhancement of microbial growth by both storage modes is largest when the substrate C:nutrient ratio is high (causing nutrient limitation after substrate addition) and the amount of added substrate is large. Moreover, storage increases biomass nutrient retention and growth more effectively when resources are supplied in a few large pulses compared to several smaller pulses (mimicking a nearly constant supply), which suggests storage to be particularly relevant in highly dynamic soil microhabitats. Overall, our results indicate that storage dynamics are most important under conditions of strong stoichiometric imbalance and may be of high ecological relevance in soil environments experiencing large variations in C and nutrient supply.

Amino acids dominate diffusive nitrogen fluxes across soil depths in acidic tussock tundra

Organic nitrogen (N) is abundant in soils, but early conceptual frameworks considered it nonessential for plant growth. It is now well recognised that plants have the potential to take up organic N. However, it is still unclear whether plants supplement their N requirements by taking up organic N in situ: at what rate is organic N diffusing towards roots and are plants taking it up? We combined microdialysis with live-root uptake experiments to measure amino acid speciation and diffusion rates towards roots of Eriophorum vaginatum. Amino acid diffusion rates (321 ng N cm^-2  h^-1 ) were c. 3× higher than those for inorganic N. Positively charged amino acids made up 68% of the N diffusing through soils compared with neutral and negatively charged amino acids. Live-root uptake experiments confirmed that amino acids are taken up by plants (up to 1 µg N g^-1  min^-1 potential net uptake). Amino acids must be considered when forecasting plant-available N, especially when they dominate the N supply, and when acidity favours proteolysis over net N mineralisation. Determining amino acid production pathways and supply rates will become increasingly important in projecting the extent and consequences of shrub expansion, especially considering the higher C : N ratio of plants relative to soil.

The global distribution and environmental drivers of aboveground versus belowground plant biomass

A poor understanding of the fraction of global plant biomass occurring belowground as roots limits our understanding of present and future ecosystem function and carbon pools. Here we create a database of root-mass fractions (RMFs), an index of plant below- versus aboveground biomass distributions, and generate quantitative, spatially explicit global maps of RMFs in trees, shrubs and grasses. Our analyses reveal large gradients in RMFs both across and within vegetation types that can be attributed to resource availability. High RMFs occur in cold and dry ecosystems, while low RMFs dominate in warm and wet regions. Across all vegetation types, the directional effect of temperature on RMFs depends on water availability, suggesting feedbacks between heat, water and nutrient supply. By integrating our RMF maps with existing aboveground plant biomass information, we estimate that in forests, shrublands and grasslands, respectively, 22%, 47% and 67% of plant biomass exists belowground, with a total global belowground fraction of 24% (20-28%), that is, 113 (90-135) Gt carbon. By documenting the environmental correlates of root biomass allocation, our results can inform model projections of global vegetation dynamics under current and future climate scenarios.

Organic substitutions aggravated microbial nitrogen limitation and decreased nitrogen-cycling gene abundances in a three-year greenhouse vegetable field

Partially substituting chemical fertilizer with organic fertilizer has substantially changed the stoichiometric imbalances of carbon (C), nitrogen (N) and phosphorus (P) between microbial communities and their available resources in agroecosystems. However, how organic substitution alters microbial nutrient limitation and then affects soil N cycle in intensive greenhouse vegetable ecosystem, remain unknown. Thus, we performed a three-year greenhouse vegetable field experiment in China with different fertilization strategies: no N fertilization, chemical N fertilization, and substituting 20% (1M4N) or 50% (1M1N) of chemical N with organic fertilizer (organic substitutions). Our results demonstrated that the microbial communities presented N limitation, accompanying with a strong N:P but a weak C:N (or P) microbial homeostasis in response to high N:P imbalance among all treatments. Organic substitutions at 1M1N and 1M4N significantly aggravated microbial N limitation and decreased the gene abundances of nitrification and denitrification by 4.7%-27.3% than that of chemical N fertilization. Microbial N limitation was strongly influenced by N:P stoichiometric imbalance illustrated from regression analysis. The N-cycling gene abundances were not only dependent on the inorganic N pool and soil physicochemical properties (i.e. pH and electrical conductivity), but also affected by microbial nutrient limitation inferred from random forest analysis. Furthermore, the 1M1N treatment performed better than the 1M4N in terms of improved crop yield and less microbial N limitation. Overall, these results highlight the importance of ecological stoichiometry in regulating soil N cycle under different fertilization strategies for intensive greenhouse vegetable ecosystem.

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-021-00793-9.

Inactive and inefficient: Warming and drought effect on microbial carbon processing in alpine grassland at depth

Subsoils contain >50% of soil organic carbon (SOC) globally yet remain under-investigated in terms of their response to climate changes. Recent evidence suggests that warmer, drier conditions in alpine grasslands induce divergent responses in SOC decomposition and carbon accrual in top- versus subsoils. However, longer term effects on microbial activity (i.e., catabolic respiration vs. anabolic growth) and belowground carbon cycling are not well understood. Here we utilized a field manipulation experiment on the Qinghai-Tibetan Plateau and conducted a 110-day soil incubation with and without ¹³ C-labeled grass litter to assess microbes' role as both SOC "decomposers" and "contributors" in the top- (0-10 cm) versus subsoils (30-40 cm) after 5 years of warming and drought treatments. Microbial mineralization of both SOC and added litter was examined in tandem with potential extracellular enzyme activities, while microbial biomass synthesis and necromass accumulation were analyzed using phospholipid fatty acids and amino sugars coupled with ¹³ C analysis, respectively. We found that warming and, to a lesser extent, drought decreased the ratio of inorganic nitrogen (N) to water-extractable organic carbon in the subsoil, intensifying N limitation at depth. Both SOC and litter mineralization were reduced in the subsoil, which may also be related to N limitation, as evidenced by lower hydrolase activity (especially leucine aminopeptidase) and reduced microbial efficiency (lower biomass synthesis and necromass accumulation relative to respiration). However, none of these effects were observed in the topsoil, suggesting that soil microbes became inactive and inefficient in subsoil but not topsoil environments. Given increasing belowground productivity in this alpine grassland under warming, both elevated root deposits and diminished microbial activity may contribute to new carbon accrual in the subsoil. However, the sustainability of plant growth and persistence of subsoil SOC pools deserve further investigation in the long term, given the aggravated N limitation at depth.

Plant intraspecific competition and growth stage alter carbon and nitrogen mineralization in the rhizosphere

Plant roots interact with rhizosphere microorganisms to accelerate soil organic matter (SOM) mineralization for nutrient acquisition. Root-mediated changes in SOM mineralization largely depend on root-derived carbon (root-C) input and soil nutrient status. Hence, intraspecific competition over plant development and spatiotemporal variability in the root-C input and nutrients uptake may modify SOM mineralization. To investigate the effect of intraspecific competition on SOM mineralization at three growth stages (heading, flowering, and ripening), we grew maize (C4 plant) under three planting densities on a C3 soil and determined in situ soil C- and N-mineralization by ¹³ C-natural abundance and ¹⁵ N-pool dilution approaches. From heading to ripening, soil C- and N-mineralization rates exhibit similar unimodal trends and were tightly coupled. The C-to-N-mineralization ratio (0.6 to 2.6) increased with N availability, indicating that an increase in N-mineralization with N depletion was driven by microorganisms mining N-rich SOM. With the intraspecific competition, plants increased specific root lengths as an efficient strategy to compete for resources. Root morphologic traits rather than root biomass per se were positively related to C- and N-mineralization. Overall, plant phenology and intraspecific competition controlled the intensity and mechanisms of soil C- and N- mineralization by the adaptation of root traits and nutrient mining.

High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils

Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked these data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C, or 35°C for 1 month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.

Organic Carbon transport model of abandoned river channels - A motif for floodplain geomorphology influencing biogeochemical swaying of arsenic

Meandering-river geomorphology, forming abandoned channels/lakes with organic carbon-burial and microbial reductive dissolution, play many crucial roles in controlling arsenic (As) fluxes in sinks such as contaminated aquifers of riverine alluvial plains across the world. Suhiya oxbow-lake in the middle alluvial plain of the River Ganga, was selected as the natural laboratory. A top-down multidisciplinary approach was chosen employing satellite imagery to analyse the annual oxbow-lake surface vegetation dynamics (Eichhornia and Hydrilla). Side-scan sonar profiles across two oxbow lakes along with River Ganga core data and vintage topographical maps, estimated the lake-sedimentation rate of 9.6 cm/yr. Organic carbon [amino acids, aromatics, lingo-phenols and lipids hydrocarbons] infiltration-based on hydrophobicity and molecular-mass was detected at different depths along the water and sedimentary column. Elemental analysis showed lake surface to groundwater the As conc. varied from (0.37 to 185 μg/l). A microbial diversity based study showed that large sized photoautotrophs Nostoc, Anabaena are replaced by Fe-oxido-reducing As-metabolizing bacteria e.g. Acidovorax, Dechloromonas and enteric organisms e.g. Enterobacter, Salmonella at bottom of water column. Based on these inferences, a conceptual organic carbon transport model was constructed to understand the preferential preservation and microbial diagenesis resulting in mobilization of As and other geogenic elements.

Experimental nitrogen fertilisation globally accelerates, then slows decomposition of leaf litter

Plant litter decomposition is a central process in the carbon (C) cycle and sensitive to ongoing anthropogenic nitrogen (N) fertilisation. Previous syntheses evaluating the effect of N fertilisation on litter decomposition relied largely on models that define a constant rate of mass loss throughout decomposition, which may mask hypothesised shifts in the effect of N fertilisation on litter decomposition dynamics. In this meta-analysis, we compared the performance of four empirical decomposition models and showed that N fertilisation consistently accelerates early-stage but slows late-stage decomposition when the model structure allows for flexibility in decomposition rates through time. Within a particular substrate, early-stage N-stimulation of decomposition was associated with reduced rates of late-stage decay. Because the products of early- vs. late-stage decomposition are stabilised in soils through distinct chemical and physical mechanisms, N-induced changes in the litter decomposition process may influence the formation and cycling of soil C, the largest terrestrial C pool.

Soil type regulates carbon and nitrogen stoichiometry and mineralization following biochar or nitrogen addition

Most studies on the effects of biochar and fertilizer on soil carbon (C) and nitrogen (N) mineralization, and microbial C and N content, are restricted to a single soil type, limiting our understanding of the interactions between these factors and microbial functions. To address this paucity in knowledge, we undertook a 3-year experiment using four contrasting soils to assess the role of peanut shell biochar and fertilizer on C and N mineralization, microbial C and N, and N stoichiometry. Across all four soils, biochar significantly (P < 0.05) increased soil carbon mineralization (C_min) and nitrogen mineralization (N_min) over three years compared to fertilizer and the control. Biochar also increased total C (C_soil) across the four soils in year 1, with the Fluvisol recording greater total C in year 2 and Phaeozem having greater total C in year 3. Biochar resulted in a higher microbial biomass C (C_mic), total N (N_soil) and microbial biomass N (N_mic); the degree of change was closely related to C_soil and N_soil. There was a positive correlation between C_mic:N_mic and C_soil:N_soil; while C_soil and C_mic increased following amendment with biochar, which reduced the soil C and N stoichiometric imbalance (N_imb) caused by the increase in the C to N ratio. However, fertilizer exacerbated the imbalance of soil C and N stoichiometry. Fertilizer also reduced the C_soil:N_soil and C_mic:N_mic ratios. Soil pH had a positive correlation with C_soil, C_mic, N_mic, C_min, N_min, C_soil:N_soil, C_mic:N_mic, and biochar increases this correlation. The soil pH was negatively correlated with C_imb:N_imb and N_soil. Fertilizer was positively correlated C_imb:N_imb and N_soil. In contrast, fertilizer N application lowered microbial biomass C:N. We conclude that biochar reduces the imbalance of soil C and N stoichiometry, whereas fertilizer increased this imbalance. Biochar had a greater impact on C and N in soils with a lower pH.

Increasing rates of long-term nitrogen deposition consistently increased litter decomposition in a semi-arid grassland

The continuing nitrogen (N) deposition observed worldwide alters ecosystem nutrient cycling and ecosystem functioning. Litter decomposition is a key process contributing to these changes, but the numerous mechanisms for altered decomposition remain poorly identified. We assessed these different mechanisms with a decomposition experiment using litter from four abundant species (Achnatherum sibiricum, Agropyron cristatum, Leymus chinensis and Stipa grandis) and litter mixtures representing treatment-specific community composition in a semi-arid grassland under long-term simulation of six different rates of N deposition. Decomposition increased consistently with increasing rates of N addition in all litter types. Higher soil manganese (Mn) availability, which apparently was a consequence of N addition-induced lower soil pH, was the most important factor for faster decomposition. Soil C : N ratios were lower with N addition that subsequently led to markedly higher bacterial to fungal ratios, which also stimulated litter decomposition. Several factors contributed jointly to higher rates of litter decomposition in response to N deposition. Shifts in plant species composition and litter quality played a minor role compared to N-driven reductions in soil pH and C : N, which increased soil Mn availability and altered microbial community structure. The soil-driven effect on decomposition reported here may have long-lasting impacts on nutrient cycling, soil organic matter dynamics and ecosystem functioning.

A multi-scale eco-evolutionary model of cooperation reveals how microbial adaptation influences soil decomposition

The decomposition of soil organic matter (SOM) is a critical process in global terrestrial ecosystems. SOM decomposition is driven by micro-organisms that cooperate by secreting costly extracellular (exo-)enzymes. This raises a fundamental puzzle: the stability of microbial decomposition in spite of its evolutionary vulnerability to “cheaters”—mutant strains that reap the benefits of cooperation while paying a lower cost. Resolving this puzzle requires a multi-scale eco-evolutionary model that captures the spatio-temporal dynamics of molecule-molecule, molecule-cell, and cell-cell interactions. The analysis of such a model reveals local extinctions, microbial dispersal, and limited soil diffusivity as key factors of the evolutionary stability of microbial decomposition. At the scale of whole-ecosystem function, soil diffusivity influences the evolution of exo-enzyme production, which feeds back to the average SOM decomposition rate and stock. Microbial adaptive evolution may thus be an important factor in the response of soil carbon fluxes to global environmental change.

Abs et al. develop a multi-scale model to explain the evolution of microbial cooperation driving the decomposition of soil organic matter. Their model shows that the evolutionary stability of decomposition depends on a combination of local extinctions, microbial dispersal, and limited soil diffusivity.

Microbes changed their carbon use strategy to regulate the priming effect in an 11-year nitrogen addition experiment in grassland

Nitrogen availability is a key factor that regulates soil priming (the strong short-term changes in microbial decomposition of soil organic carbon after addition of fresh carbon resources); however, how soil priming changes under nitrogen addition is unclear. In this study, we collected soils from a grassland with 11-year history of nitrogen addition (0, 60, 120, and 240 kg N ha^-1 yr^-1 NH₄NO₃), and the soils were incubated for 6 weeks to estimate the direction and magnitude of soil priming and the underlying microbial carbon use strategy. We found glucose addition triggered a positive priming effect among all the treatments; however, the magnitude of the positive priming did not change under nitrogen addition. The stable soil organic carbon content under different nitrogen addition levels might support the no significant change in the magnitude of those positive priming. Using DNA stable-isotope probing (DNA-SIP), we found that bacterial and fungal taxa consuming the added glucose were different in different nitrogen addition levels. The relative abundance of the K-strategist Acidobacteria increased with increasing nitrogen addition levels, while the r-strategist Firmicutes decreased with increasing nitrogen addition levels. Our results indicated microbial taxa exhibited carbon use plasticity, with most taxa altering their use of glucose under nitrogen addition.

Extrinsic Factors Shaping the Skin Microbiome

Human skin, our most environmentally exposed organ, is colonized by a vast array of microorganisms constituting its microbiome. These bacterial communities are crucial for the fulfillment of human physiological functions such as immune system modulation and epidermal development and differentiation. The structure of the human skin microbiome is established during the early life stages, starting even before birth, and continues to be modulated throughout the entire life cycle, by multiple host-related and environmental factors. This review focuses on extrinsic factors, ranging from cosmetics to the environment and antibacterial agents, as forces that impact the human skin microbiome and well-being. Assessing the impact of these factors on the skin microbiome will help elucidate the forces that shape the microbial populations we coexist with. Furthermore, we will gain additional insight into their tendency to stimulate a healthy environment or to increase the propensity for skin disorder development.