Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction

Challenges in upscaling laboratory studies to ecosystems in soil microbiology research

Soil microbiology has entered into the big data era, but the challenges in bridging laboratory-, field-, and model-based studies of ecosystem functions still remain. Indeed, the limitation of factors in laboratory experiments disregards interactions of a broad range of in situ environmental drivers leading to frequent contradictions between laboratory- and field-based studies, which may consequently mislead model development and projections. Upscaling soil microbiology research from laboratory to ecosystems represents one of the grand challenges facing environmental scientists, but with great potential to inform policymakers toward climate-smart and resource-efficient ecosystems. The upscaling is not only a scale problem, but also requires disentangling functional relationships and processes on each level. We point to three potential reasons for the gaps between laboratory- and field-based studies (i.e., spatiotemporal dynamics, sampling disturbances, and plant-soil-microbial feedbacks), and three key issues of caution when bridging observations and model predictions (i.e., across-scale effect, complex-process coupling, and multi-factor regulation). Field-based studies only cover a limited range of environmental variation that must be supplemented by laboratory and mesocosm manipulative studies when revealing the underlying mechanisms. The knowledge gaps in upscaling soil microbiology from laboratory to ecosystems should motivate interdisciplinary collaboration across experimental, observational, theoretic, and modeling research.

Synergistic effects of diazotrophs and arbuscular mycorrhizal fungi on soil biological nitrogen fixation after three decades of fertilization

Biological nitrogen (N) fixation (BNF) via diazotrophs is an important ecological process for the conversion of atmospheric N to biologically available N. Although soil diazotrophs play a dominant role in BNF and arbuscular mycorrhizal fungi (AMF) serve as helpers to favor BNF, the response of soil BNF and diazotrophic communities to different long-term fertilizations and the role of AMF in diazotrophs-driven BNF are poorly understood. Herein, a 33-year fertilization experiment in a wheat-maize intercropping system was conducted to investigate the changes in soil BNF rates, diazotrophic and AMF communities, and their interactions after long-term representative fertilization (chemical fertilizer, cow manure, wheat straw, and green manure). We found a remarkable increase in soil BNF rates after more than three decades of fertilization compared with nonfertilized soil, and the green manure treatment rendered the highest enhancement. The functionality strengthening was mainly associated with the increase in the absolute abundance of diazotrophs and AMF and the relative abundance of the key ecological cluster of Module #0 (gained from the co-occurrence network of diazotrophic and AMF species) with dominant diazotrophs such as Skermanella and Azospirillum. Furthermore, although the positive correlations between diazotrophs and AMF were reduced under long-term organic fertilization regimes, green manuring could reverse the decline within Module #0, and this had a positive relationship with the BNF rate. This study suggests that long-term fertilization could promote N fixation and select specific groups of N fixers and their helpers in certain areas. Our work provides solid evidence that N fixation and certain groups of diazotrophic and AMF taxa and their interspecies relationship will be largely favored after the fertilized strategy of green manure.

Understory species composition mediates soil greenhouse gas fluxes by affecting bacterial community diversity in boreal forests

Introduction

Plant species composition in forest ecosystems can alter soil greenhouse gas (GHG) budgets by affecting soil properties and microbial communities. However, little attention has been paid to the forest types characterized by understory vegetation, especially in boreal forests where understory species contribute significantly to carbon and nitrogen cycling.

Method

In the present study, soil GHG fluxes, soil properties and bacterial community, and soil environmental conditions were investigated among three types of larch forest [Rhododendron simsii-Larix gmelinii forest (RL), Ledum palustre-Larix gmelinii forest (LL), and Sphagnum-Bryum-Ledum palustre-Larix gmelinii forest (SLL)] in the typical boreal region of northeast China to explore whether the forest types characterized by different understory species can affect soil GHG fluxes.

Results

The results showed that differences in understory species significantly affected soil GHG fluxes, properties, and bacterial composition among types of larch forest. Soil CO₂ and N₂O fluxes were significantly higher in LL (347.12 mg m^-2 h^-1 and 20.71 μg m^-2 h^-1) and RL (335.54 mg m^-2 h^-1 and 20.73 μg m^-2 h^-1) than that in SLL (295.58 mg m^-2 h^-1 and 17.65 μg m^-2 h^-1), while lower soil CH₄ uptake (-21.07 μg m^-2 h^-1) were found in SLL than in RL (-35.21 μg m^-2 h^-1) and LL (-35.85 μg m^-2 h^-1). No significant differences between LL and RL were found in soil CO₂, CH₄, and N₂O fluxes. Soil bacterial composition was mainly dominated by Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi among the three types of larch forest, while their abundances differed significantly. Soil environmental variables, soil properties, bacterial composition, and their interactions significantly affected the variations in GHG fluxes with understory species. Specifically, structural equation modeling suggested that soil bacterial composition and temperature had direct close links with variations in soil GHG fluxes among types of larch forest. Moreover, soil NO₃ ^--N and NH₄ ⁺ - N content also affected soil CO₂, CH₄, and N₂O fluxes indirectly, via their effects on soil bacterial composition.

Discussion

Our study highlights the importance of understory species in regulating soil GHG fluxes in boreal forests, which furthers our understanding of the role of boreal forests in sustainable development and climate change mitigation.

Microbial community diversity and function analysis of Aconitum carmichaelii Debeaux in rhizosphere soil of farmlands in Southwest China

Understanding how microbial communities affect plant growth is crucial for sustainable productivity and ecological health. However, in contrast with the crop system, there is limited information on the microbial community associated with the medicinal plant. We observed that altitude was the most influential factor on the soil microbial community structures of Aconitum carmichaelii Debeaux. For community composition, bacterial reads were assigned to 48 phyla, with Proteobacteria, Acidobacteriota, and Actinobacteriota being the dominant phyla. The fungal reads were assigned to seven phyla, and Ascomycota was the predominant phylum detected in most groups. The four dominant phyla were categorized as keystone taxa in the co-occurrence networks, suggesting that they may be involved in soil disease suppression and nutrient mobility. Bacterial co-occurrence networks had fewer edges, lower average degree, and lower density at YL1, HQ1, HQ2, BC, and DL than fungal networks, creating less intricate rhizosphere network patterns. Furthermore, the bacterial and fungal communities showed strong distance decay of similarity across the sampling range. Overall, this study improves our understanding of regulating rhizosphere microbial communities in soil systems and also provides potential production strategies for planting A. carmichaelii.

Improved tolerance of apple plants to drought stress and nitrogen utilization by modulating the rhizosphere microbiome via melatonin and dopamine

This study explored the contributions of melatonin and dopamine to the uptake and utilization of nitrogen and the formation of rhizosphere microbial communities in 'Tianhong 2'/M. hupehensis, with the goal improving plant resistance to drought stress. Drought stress was formed by artificially controlling soil moisture content. And melatonin or dopamine solutions were applied to the soil at regular intervals for experimental treatment. After 60 days of treatment, plant indices were determined and the structure of the rhizosphere microbial community was evaluated using high-throughput sequencing technology. The findings revealed two ways through which melatonin and dopamine alleviate the inhibition of growth and development caused by drought stress by promoting nitrogen uptake and utilization in plants. First, melatonin and dopamine promote the absorption and utilization of nitrogen under drought stress by directly activating nitrogen transporters and nitrogen metabolism-related enzymes in the plant. Second, they promote the absorption of nitrogen by regulating the abundances of specific microbial populations, thereby accelerating the transformation of the soil nitrogen pool to available nitrogen that can be absorbed directly by plant roots and utilized by plants. These findings provide a new framework for understanding how melatonin and dopamine regulate the uptake and utilization of nitrogen in plants and improve their ability to cope with environmental disturbances.

Corner Flows Induced by Surfactant-Producing Bacteria Bacillus subtilis and Pseudomonas fluorescens

A mechanistic understanding of bacterial spreading in soil, which has both air and water in angular pore spaces, is critical to control pathogenic contamination of soil and to design bioremediation projects. A recent study (J. Q. Yang, J. E. Sanfilippo, N. Abbasi, Z. Gitai, et al., Proc Natl Acad Sci U S A 118:e2111060118, 2021, https://doi.org/10.1073/pnas.2111060118) shows that Pseudomonas aeruginosa can self-generate flows along sharp corners by producing rhamnolipids, a type of biosurfactants that change the hydrophobicity of solid surfaces. We hypothesize that other types of biosurfactants and biosurfactant-producing bacteria can also generate corner flows. Here, we first demonstrate that rhamnolipids and surfactin, biosurfactants with different chemical structures, can generate corner flows. We identify the critical concentrations of these two biosurfactants to generate corner flow. Second, we demonstrate that two common soil bacteria, Pseudomonas fluorescens and Bacillus subtilis (which produce rhamnolipids and surfactin, respectively), can generate corner flows along sharp corners at the speed of several millimeters per hour. We further show that a surfactin-deficient mutant of B. subtilis cannot generate corner flow. Third, we show that, similar to the finding for P. aeruginosa, the critical corner angle for P. fluorescens and B. subtilis to generate corner flows can be predicted from classic corner flow theories. Finally, we show that the height of corner flows is limited by the roundness of corners. Our results suggest that biosurfactant-induced corner flows are prevalent in soil and should be considered in the modeling and prediction of bacterial spreading in soil. The critical biosurfactant concentrations we identify and the mathematical models we propose will provide a theoretical foundation for future predictions of bacterial spreading in soil. IMPORTANCE The spread of bacteria in soil is critical in soil biogeochemical cycles, soil and groundwater contamination, and the efficiency of soil-based bioremediation projects. However, the mechanistic understanding of bacterial spreading in soil remains incomplete due to a lack of direct observations. Here, we simulate confined spaces of hydrocarbon-covered soil using a transparent material with similar hydrophobicity and visualize the spread of two common soil bacteria, Pseudomonas fluorescens and Bacillus subtilis. We show that both bacteria can generate corner flows at the velocity of several millimeters per hour by producing biosurfactants, soap-like chemicals. We provide quantitative equations to predict the critical corner angle for bacterial corner flow and the maximum distance of the corner spreading. We anticipate that bacterial corner flow is prevalent because biosurfactant-producing bacteria and angular pores are common in soil. Our results will help improve predictions of bacterial spreading in soil and facilitate the design of soil-related bioremediation projects.

Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China

The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 10⁷ copies) followed by NirK (2.71 × 10⁶ copies), AOA (1.97 × 10⁶ copies), and AOB (7.38 × 10⁴ copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.

Contrasted speciation distribution of toxic metal(loid)s and microbial community structure in vanadium-titanium magnetite tailings under dry and wet disposal methods

Tailing disposal technologies such as dry and wet disposal methods have a profound effect on the ecosystem of mining areas. However, the chemical speciation of metal(loid)s and microbial community structure in tailings under different disposal methods are still poorly understood. Here we compared the bioavailable fraction of metal(loid)s and the microbial community in vanadium-titanium (V-Ti) magnetite tailing profiles derived from dry and wet stockpiled methods. In wet tailings, the bioavailability of Cr, Cu, Mn, Ni, V, and Zn was higher than that in dry tailings as identified by BCR sequential extraction. Especially for Cu and Ni, the oxidizable fraction was the predominant fraction except the residual fraction, accounting for 37.2-59.0% and 23.2-36.6% of the total concentration in wet tailings, respectively. Based on 16 S rRNA high-throughput sequencing, totally 12 indicator bacterial taxa were detected in dry tailings against 68 in wet tailings. As the biomarkers in wet tailings, genera Sulfuricurvum, Geobacter, and Pseudomonas were expected to be applied to the transformation of metal(loid)s in the tailings. Our results emphasize the importance of dehydration treatment of tailings before stockpiling to minimize the environmental risks caused by toxic metal(loid)s, and provide insights into the engineering application of microbial technologies in V-Ti magnetite tailing area.

Responses of soil respiration and microbial community structure to fertilizer and irrigation regimes over 2 years in temperate vineyards in North China

Fertilizer and irrigation regimes can profoundly affect soil carbon (C) emissions, which influence soil organic carbon (SOC) storage. However, information regarding the effects of fertilizer and irrigation management on the components of soil respiration (Rs) and the underlying microbial community characteristics in vineyard ecosystems remains limited. Therefore, a 2-year field experiment was conducted in a wine-grape vineyard (WGV) and a table-grape vineyard (TGV). Each vineyard included two fertilizer and irrigation regimes: farmers' practice (FP) and recommended practice (RP). The trenching method was employed to separate Rs into heterotrophic respiration (Rh) and autotrophic respiration (Ra). Additionally, the SOC storage and soil microbial community structure at 0-20 cm soil depth were determined after the 2-year experiment. The results showed that the fertilizer and irrigation regimes caused no effect on Ra. Compared with the FP treatment in WGV and TGV, the RP treatment significantly (P < 0.05) decreased the average daily Rh by 15.13 % and 17.11 %, which contributed to the annual Rs values at the whole-vineyard scale decreased by 8.93 % and 11.78 %, respectively. Besides, compared with the initial value, the SOC storage under RP treatment were effectively increased by 6.39 % and 6.33 % in WGV and TGV, respectively. Low annual total Rh was partially ascribed to the significant (P < 0.05) decline in Proteobacteria and Bacteroidetes relative abundance, thus reducing the decomposition rate of SOC. Compared with WGV, the fertilizer and water input was higher in the TGV, which resulted in the annual total Rs and Rh values at the whole-vineyard scale was increased by 11.53 % and 15.74 %, respectively, while the annual total Ra was decreased by 18.83 % due to the lower grapevine density and more frequent summer pruning. Overall, RP treatment was found to be a suitable strategy for reducing soil C emissions and benefiting SOC storage in vineyards around North China.

Crop-type-driven changes in polyphenols regulate soil nutrient availability and soil microbiota

Crop rotation is a typical agronomic practice to mitigate soil deterioration caused by continuous cropping. However, the mechanisms of soil biotic and abiotic factors in response to different cropping patterns in acidic and polyphenol-rich tea nurseries remain unclear. In this study, the composition and function of microbial communities were comparatively investigated in soils of tea seedlings continuously planted for 2 years (AC: autumn-cutting; SC: summer-cutting) and in soils rotation with strawberries alternately for 3 years (AR: autumn-cutting). The results showed that AR significantly improved the survival of tea seedlings but greatly reduced the contents of soil polyphenols. The lower soil polyphenol levels in AR were associated with the decline of nutrients (SOC, TN, Olsen-P) availability, which stimulates the proliferation of nutrient cycling-related bacteria and mixed-trophic fungi, endophytic fungi and ectomycorrhizal fungi, thus further satisfying the nutrient requirements of tea seedlings. Moreover, lower levels of polyphenols facilitated the growth of plant beneficial microorganisms (Bacillus, Mortierella, etc.) and suppressed pathogenic fungi (Pseudopestalotiopsis, etc.), creating a more balanced microbial community that is beneficial to plant health. Our study broadens the understanding of the ecological role of plant secondary metabolites and provides new insights into the sustainability of tea breeding.

Soil Microbial Diversity and Community Composition in Rice-Fish Co-Culture and Rice Monoculture Farming System

Simple Summary

The integration of fish in rice fields can influence the diversity and structural composition of soil microbial communities. Therefore, soil microorganisms between rice–fish co-culture (RF) and rice monoculture (MC) were compared. The key findings revealed that Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes were the most dominant taxa across both paddy fields. The most abundant genus in MC belonged to Anaeromyxobacter, whereas that in RF was Bacillus. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF. Phosphatase, β-glucosidase, cellulase, and urease enzymes were detected in both paddy fields. However, a 2-year conversion from organic rice to rice–fish co-culture may not be long enough to significantly alter alpha diversity indices.

Abstract

Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility.

Comparative study of pyrochar and hydrochar on peanut seedling growth in a coastal salt-affected soil of Yellow River Delta, China

Biochar (i.e., pyrochar and hydrochar) application is a promising strategy to improve soil quality and productivity. However, the comparison of biochars with different carbonization methods and feedstocks for the plant growth in the coastal salt-affected soil remains limited. In this study, a 30-day microcosmic experiment was conducted to compare the effects of pyrochars and hydrochars derived from reed straw (RPC and RHC) and cow manure (CPC and CHC) on the peanut (Arachis hypogaea L.) seedling growth in a coastal salt-affected soil of Yellow River Delta, China. The results showed that RPC, CHC and CPC significantly elevated fresh shoot weight by 67.77%-89.37%, whereas the RHC amendment showed little effect. The malondialdehyde contents in peanut seedling leaves were significantly declined by 25.28%-35.51% with pyrochar and hydrochar amendments, which might be associated with the enhanced proline contents and K/Na ratios. The stimulation of certain phytohormones (i.e., indole-3-acetic acid, zeatin riboside, gibberellic acid 3) in peanut seedlings with pyrochar and hydrochar amendments might be attributed to the growth enhancement. RPC, CPC and CHC improved the soil properties and fertility such as cation-exchange capacity (CEC), total nitrogen, and available potassium and water holding capacity (WHC) of the coastal salt-affected soil. However, RHC not only significantly decreased soil CEC and WHC, but also increased soil exchangeable sodium percentage. The abundances of soil beneficial bacteria, such as f_Gemmatimonadacea, Sphingomonas, Blastococcus and Lysobacter were enhanced by RPC, CHC and CPC amendments, which were mainly associated with the increased WHC and CEC. Fungal community was less sensitive to pyrochar and hydrochar amendments than bacterial community according to the relative abundance and diversity, and beneficial fungi, such as Oidiodendron and Sarocladium were enriched in the CHC soil. Overall, the application of RPC, CHC and CPC showed greater potentials for the enhancement of peanut growth in a coastal salt-affected soil.

Salt-tolerant endophytic bacterium Enterobacter ludwigii B30 enhance bermudagrass growth under salt stress by modulating plant physiology and changing rhizosphere and root bacterial community

Osmotic and ionic induced salt stress suppresses plant growth. In a previous study, Enterobacter ludwigii B30, isolated from Paspalum vaginatum, improved seed germination, root length, and seedling length of bermudagrass (Cynodon dactylon) under salt stress. In this study, E. ludwigii B30 application improved fresh weight and dry weight, carotenoid and chlorophyll levels, catalase and superoxide dismutase activities, indole acetic acid content and K⁺ concentration. Without E. ludwigii B30 treatment, bermudagrass under salt stress decreased malondialdehyde and proline content, Y(NO) and Y(NPQ), Na⁺ concentration, 1-aminocyclopropane-1-carboxylate, and abscisic acid content. After E. ludwigii B30 inoculation, bacterial community richness and diversity in the rhizosphere increased compared with the rhizosphere adjacent to roots under salt stress. Turf quality and carotenoid content were positively correlated with the incidence of the phyla Chloroflexi and Fibrobacteres in rhizosphere soil, and indole acetic acid (IAA) level was positively correlated with the phyla Actinobacteria and Chloroflexi in the roots. Our results suggest that E. ludwigii B30 can improve the ability of bermudagrass to accumulate biomass, adjust osmosis, improve photosynthetic efficiency and selectively absorb ions for reducing salt stress-induced injury, while changing the bacterial community structure of the rhizosphere and bermudagrass roots. They also provide a foundation for understanding how the bermudagrass rhizosphere and root microorganisms respond to endophyte inoculation.

Successive walnut plantations alter soil carbon quantity and quality by modifying microbial communities and enzyme activities

Knowledge of the spatial–temporal variations of soil organic carbon (SOC) quantity and quality and its microbial regulation mechanisms is essential for long-term SOC sequestration in agroecosystems; nevertheless, this information is lacking in the process of walnut plantations. Here, we used the modified Walkley-Black method, phospholipid fatty acid analysis, and micro-plate enzyme technique to analyze the evolution of SOC stocks and quality/lability as well as microbial communities and enzyme activities at different soil depths in walnut plantations with a chronosequence of 0-, 7-, 14-, and 21-years in the Eastern Taihang Mountains, China. The results indicated that long-term walnut plantations (14-and 21-years) enhanced SOC stocks, improved SOC quality/lability (as indicated by the lability index), and promoted microbial growth and activities (i.e., hydrolase and oxidase activities) in the 0–40 cm soil layers. Besides, these above-mentioned SOC-and microbial-related indices (except for oxidase activities) decreased with increasing soil depths, while oxidase activities were higher in deeper soils (40–60 cm) than in other soils (0–40 cm). The partial least squares path model also revealed that walnut plantation ages and soil depths had positive and negative effects on microbial attributes (e.g., enzyme activities, fungal and bacterial communities), respectively. Meanwhile, the SOC stocks were closely related to the fungal community; meanwhile, the bacterial community affected SOC quality/liability by regulating enzyme activities. Comprehensively, long-term walnut plantations were conducive to increasing SOC stocks and quality through altering microbial communities and activities in the East Taihang Mountains in Hebei, China.

Microbial community structure and functional genes drive soil priming effect following afforestation

Afforestation substantially modifies native soil organic carbon (SOC) decomposition via plant carbon inputs (the priming effect), and in turn, triggers vital biogeochemical processes that influence the regulation of soil carbon dynamics. Soil microbes are crucial in regulating the direction and magnitude of the priming effect. In the present study, we performed metagenomic sequencing and ¹³C-glucose labeling analyses of microbial communities and priming effects across a Robinia pseudoacacia afforestation chronosequence (14-, 20-, 30-, and 45-year-old stands) in the Loess Plateau in China, with adjacent farmland being selected as a control. Our results revealed that the cumulative priming effect across five sites along the afforestation chronosequence initially increased and approached a peak value in the 20-year-old stand, after which it declined. The priming effect was predominantly driven by the microbial community structure (i.e., the fungal-to-bacterial ratios and relative abundances of Proteobacteria and Actinobacteria), and stable C decomposition genes and C-degrading enzymes. Specifically, among the key functional genes correlated with priming effect, which were identified in orders Rhizobiales and Pseudonocardiales, considerably promoted SOC priming. Overall, our findings indicate that afforestation alters soil microbial community structure and function, particularly with respect to enhancing stable soil C decomposition genes, which may promote SOC priming. The findings of the present study could enhance our understanding of fresh C input-induced changes associated with C mineralization in the context of the revegetation of ecologically fragile areas.

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.

Appropriate Irrigation and Fertilization Regime Restrain Indigenous Soil Key Ammonia-Oxidizing Archaeal and Bacterial Consortia to Mitigate Greenhouse Gas Emissions

Harnessing an ammonia-oxidizing microbiome has become an increasingly attractive form of management for mitigating greenhouse gas emissions in rice paddies; however, the relationship between greenhouse gas emissions and ammonia-oxidizing microbiomes, using a nitrogen application and irrigation regime, has not been well investigated. To decipher which of (and how) the specific mmonia-oxidizing bacterial species drive the greenhouse gas CH4 and N2O emissions, a field experiment with varying nitrogen application and irrigation regimes was initiated to investigate the succession of key bacterial consortia associated with GHG emissions. The results showed that water-saving irrigation (AWD) significantly increased NO3-N and NH4+-N concentrations, compared with conventional irrigation (FDF), whereas (total nitrogen) TN was little higher in FDF (1.38 g kg−1) compared with the AWD (1.36 g kg−1). During the rice-growing season, CH4 emissions ascended speedily, and emissions peaked at maximum values of 3.32 and 4.41 ug mg−2 h−1 on day 5 in FDF and AWD irrigation regimes, respectively, and then they rapidly decreased during the midseason period, maintaining a relatively low emission rate until the rice was harvested. The patterns of N2O emission fluxes had the same tendencies with N fertilization. Putative key taxa, such as Flavobacterium, Massilia, Arenimonas, Novosphingobium, Pseudomonas, exhibited significant positive relationships with higher GHG emissions, suggesting that they make particularly obvious contributions to N2O emissions. These putative taxa should be considered when designing a high nitrogen application and irrigation strategy. As such, the nitrogen application of N180, and the irrigation regimes of water-saving irrigation, are recommended methods for N conservation and the mitigation of greenhouse gas emissions in rice paddies.

Salinity Effects on Microbial Derived-C of Coastal Wetland Soils in the Yellow River Delta

Microorganisms play a crucial role in regulating the turnover and transformation of soil organic carbon (SOC), whereas microbial contribution to SOC formation and storage is still unclear in coastal wetlands. In this study, we collected topsoil (0–20 cm) with 7 salinity concentrations and explored the shifts in microbial residues [represented by amino sugar (AS)] and their contribution to the SOC pool of coastal wetlands in the Yellow River delta. The gradually increasing soil salinity reduced soil water content (SWC), SOC, and soil nitrogen (N), especially in high salinity soils of coastal wetlands. Total ASs and their ratio to SOC, respectively, decreased by 90.56 and 66.35% from low salinity to high salinity soils, indicating that coastal wetlands with high salinity restrained microbial residue accumulation and microbial residue-C retention in the SOC pool. Together with redundancy analysis and path analysis, we found that SWC, pH, SOC, soil N, and glucosamine/muramic arid were positively associated with the ratio of ASs to SOC. The higher available soil resource (i.e., water, C substrate, and nutrient) increased microbial residue accumulation, promoting microbial derived-C contribution to SOC in low salinity coastal wetlands. The greatly decreased microbial residue contribution to SOC might be ascribed to microbial stress strategy and low available C substrate in coastal wetlands with high salinity concentration. Additionally, the gradually increasing salinity reduced fungal residue contribution to SOC but did not change bacterial residue contribution to SOC. These findings indicated that changed fungal residues would substantially influence SOC storage. Our study elucidates microbial contribution to SOC pool through residue reservoir in coastal wetlands and pushes microbial metabolites to a new application in global wetland SOC cycling.

Relevance of the microbial community to Sb and As biogeochemical cycling in natural wetlands

Mining activities lead to elevated levels of antimony (Sb) and arsenic (As) in river systems, having adverse effects on the aquatic environment and human health. Microbes inhabiting river sediment can mediate the transformation of Sb and As, thus changing the toxicity and mobility of Sb and As. Compared to river sediments, natural wetlands could introduce distinct geochemical conditions, leading to the formation of different sedimentary microbial compositions between river sediments and wetland sediments. However, whether such changes in microbial composition could influence the microbially mediated geochemical behavior of Sb or As remains poorly understood. In this study, we collected samples from a river contaminated by Sb tailings and a downstream natural wetland to study the influence of microorganisms on the geochemical behavior of Sb and As after the Sb/As-contaminated river entered the natural wetland. We found that the microbial compositions in the natural wetland soil differed from those in the river sediment. The Sb/As contaminant components (Sb(III), As(III), As(V), As_exe) and nutrients (TC) were important determinants of the difference in the compositions of the microbial communities in the two environments. Taxonomic groups were differentially enriched between the river sediment and wetland soil. For example, the taxonomic groups Xanthomonadales, Clostridiales and Desulfuromonadales were important in the wetland and were likely to involve in Sb/As reduction, sulfate reduction and Fe(III) reduction, whereas Burkholderiales, Desulfobacterales, Hydrogenophilales and Rhodocyclales were important taxonomic groups in the river sediments and were reported to involve in Sb/As oxidation and sulfide oxidation. Our results suggest that microorganisms in both river sediments and natural wetlands can affect the geochemical behavior of Sb/As, but the mechanisms of action are different.

Environmental stress-discriminatory taxa are associated with high C and N cycling functional potentials in dryland grasslands

Increasing environmental stress strongly affects soil microbial communities, but the responses of the microbial assembly and the functional potential of the dominant microbial community in the presence of environmental stress in drylands are still poorly understood. Here, we undertook a broad appraisal of the abundance, diversity, similarity, community assembly, network properties and functions of soil microbiomes in 82 dryland grasslands along environmental gradients. We found that the bacterial and fungal diversity and community similarity showed different sensitivities to environmental stress (decreased mean annual precipitation (MAP) and soil nutrient levels and increased soil pH), and MAP was the most important factor influencing microbial community patterns. In addition, the dominant subcommunity of both bacteria and fungi was more sensitive to environmental stress than the nondominant subcommunity. Although increasing environmental stress decreased microbial phylogenetic clustering, it had no effects on the stochastic and deterministic assembly process balance. Moreover, we identified 101 bacterial and 34 fungal environmental stress-discriminatory taxa that were sensitive to environmental stress, and these bacterial markers showed a high correlation with the abundance of carbon (C) and nitrogen (N) cycling-related genes, whereas the taxa classified as connectors in the network were mainly correlated with C degradation genes. Our study shows that the different responses of bacteria and fungi to environmental stress bring challenges to predicting microbial function, but a relatively small number of taxa play an important role in driving C and N cycling-related functional genes, indicating that identifying an organism's phenotypic characteristics or traits of key taxa may improve our knowledge of the microbial response to ongoing global changes.

Nitrogen availability mediates the priming effect of soil organic matter by preferentially altering the straw carbon-assimilating microbial community

Straw incorporation into soil increases carbon (C) sequestration but can induce priming effects (PE), the enhanced breakdown of soil organic matter. The direction and magnitude of PE and the consequences for the C balance induced by straw addition depend on nitrogen (N) availability and soil management history. Using ¹³C-labeled maize straw, we conducted a 56-day incubation to determine the dynamics of PE and the underlying microbial mechanisms after straw and/or mineral N addition to three soils with contrasting cultivation and fertilization histories, i) unfertilized soil (Unfertilized), ii) 8 years farmyard manure amended soil (Manured), and iii) abandoned cropland soil (Abandoned). ¹³C-PLFAs (phospholipid fatty acids) were analyzed to identify microbial groups utilizing straw and to explore their contribution to the PE. Straw addition increased microbial biomass (MBC), activities of enzymes related to the C and N cycles, and changed microbial community composition. SOC decomposition was enhanced by microbes activated by straw addition, leading to a positive cumulative PE ranging from 494 to 789 μg C g^-1 soil. The magnitude of positive PE and straw decomposition in the manured soil was higher than that in the unfertilized and abandoned soils due to larger MBC and higher enzyme activities, resulting in a lower net SOC gain. Compared with straw only, the combination of straw addition with N fertilizer did not influence MBC, but increased positive PE (average increase of 18.1%) and straw decomposition (17.1%), further limiting SOC gain. ¹³C-labeled fungi: bacteria ratios and Gram-positive (G+): negative (G-) bacteria ratios increased with the increasing PE after N fertilization, but soil-derived (un-labeled) PLFAs remained stable. Random forest analysis further showed that straw C-assimilating microbial attributes are important predictors in driving the greater PE after N addition. Our study highlights the importance of straw C-assimilating fungi and G+ bacteria in mediating N-induced PE in arable soils.

Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale

Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth's terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.

Insight into how fertilization strategies increase quality of grape (Kyoho) and shift microbial community

Organic and bioorganic fertilizers were increasingly used for agricultural soil. However, little is known on what kind of organic fertilizer application strategies can promote grape production well and how appropriate fertilization strategies improve soil properties and shift microbial community. This study investigated the improvement in soil physicochemical properties as well as their relations with microbial community structure and grape quality under different fertilization strategies. Our results found that (bio)organic fertilizer (CF1, CF2, and BF) especially combined application of organic and bioorganic fertilization (CBF) had smaller effects on electrical conductivity (EC) and pH, while it improved soil nutrients including N, P, K, and organic matter (OM) well, thereby promoting the grape quality comparing to the group without any fertilizer (CK) and with chemical fertilizer (NPK). Especially, the concentrations of Cr, Hg, Zn, and Cu were reduced by 13.63%, 12.50%, 12.52%, and 11.75% in CBF, respectively. Additionally, CF1, CF2, and BF, especially CBF, optimized the communities' composition and increased the abundance of some plant probiotics such as Solirubrobacter and Lysobacter. Nevertheless, excessive application of organic fertilizer derived from livestock manure could cause the accumulation of heavy metals such as Zn and Cu in soil and leaves, which could further influence the grape quality. Additionally, the structure of microbial communities was also changed possibly because some bacterial genera showed distinct adaptability to the stress of heavy metals or the utilization capacity of N, P, K, and OM. Our results demonstrated that combined application of organic and bioorganic fertilization showed a great influence on soil physicochemical properties, whose positive changes could further optimize microbial communities and facilitate the promotion of grape quality.

Microbial Community Changes in 26,500-Year-Old Thawing Permafrost

Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.

Possible effects of temperature on bacterial communities in the rhizosphere of rice under different climatic regions

Global warming is an indisputable fact. However, the effect of warming on the rhizosphere bacterial community of crops is not well understood. Therefore, we carried out pot experiments with three rice (Oryza sativa L.) varieties in black soil across three climatic regions of northeast China to simulate temperature change, and analyzed the response of the rhizosphere bacterial community to different temperatures. Results showed that climate had stronger effects on rhizosphere bacterial communities than rice variety. The rhizosphere bacterial diversity differed significantly among the three climatic regions and positively correlated with the mean daily average temperature (MAveT), mean daily maximum temperature (MMaxT), and mean daily minimum temperature (MMinT), and negatively correlated with the daily temperature range (DTR). Principal co-ordinate analysis revealed that bulk soil bacterial communities maintained a high similarity across the three climatic regions, while rhizosphere bacterial communities notably varied. This change was significantly correlated with MAveT, MMaxT, MMinT, and DTR. Compared with bulk soil, Proteobacteria and Bacteroidetes were enriched in the rhizosphere, while Actinobacteria was depleted. Moreover, these changes were strengthened by increasing the temperature and decreasing DTR. Additionally, correlation analysis revealed that changes in rhizosphere bacterial communities were closely related to the formation of rice yields. Our study revealed that the increasing temperature indirectly reshapes the rhizosphere bacterial community that may promote rice production in areas with lower temperatures.

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO₂  × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO₂ fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO₂ concentration. Our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.

Theoretical design and process control of neonicotinoids insecticides suitable for synergistic degradation with the rubisco enzyme from rhizobia and carbon-fixing bacteria in soil

In this study, we studied and developed the modification schemes of environmentally friendly substitutes of neonicotinoid insecticides (NNIs) along with the regulatory measures that effectively enhanced the synergistic degradation of NNIs by soil rhizobia and carbon-fixing bacteria. Firstly, the binding ability of NNIs to the two key proteins was characterized by molecular docking; secondly, the mean square deviation decision method, which is a comprehensive evaluation method, was used to investigate the binding ability of NNI molecules with the two Rubisco rate-limiting enzymes. The three-dimensional quantitative structure-activity relationship (3D-QSAR) model was established for the synergistic degradation and single effect of rhizobia and carbon-fixing bacteria. Finally, after combining the 3D-QSAR model with a contour map analysis of the synergistic degradation effect of soil rhizobia and carbon-fixing bacteria, 102 NNI derivatives were designed. Flonicamid-36 and other four NNI derivatives passed the functional and environmentally friendly evaluation. Taguchi orthogonal experiment and factorial experiment-assisted molecular dynamics method were used to simulate the effects of 32 regulation schemes on the synergistic degradation of NNIS and its derivatives by rhizobia and carbon fixing bacteria. The synergistic degradation capacity of soil rhizobia and carbon-fixing bacteria was increased to 33.32% after right nitrogen supplementation. This indicated that supplementing the correct amount of nitrogen in the soil environment was beneficial to the microbial degradation of NNIs and their derivatives.

Microbial traits determine soil C emission in response to fresh carbon inputs in forests across biomes

Soil priming is a microbial-driven process, which determines key soil-climate feedbacks in response to fresh carbon inputs. Despite its importance, the microbial traits behind this process are largely undetermined. Knowledge of the role of these traits is integral to advance our understanding of how soil microbes regulate carbon (C) emissions in forests, which support the largest soil carbon stocks globally. Using metagenomic sequencing and ¹³ C-glucose, we provide unprecedented evidence that microbial traits explain a unique portion of the variation in soil priming across forest biomes from tropical to cold temperature regions. We show that microbial functional profiles associated with the degradation of labile C, especially rapid simple sugar metabolism, drive soil priming in different forests. Genes involved in the degradation of lignin and aromatic compounds were negatively associated with priming effects in temperate forests, whereas the highest level of soil priming was associated with β-glucosidase genes in tropical/subtropical forests. Moreover, we reconstructed, for the first time, 42 whole bacterial genomes associated with the soil priming effect and found that these organisms support important gene machinery involved in priming effect. Collectively, our work demonstrates the importance of microbial traits to explain soil priming across forest biomes and suggests that rapid carbon metabolism is responsible for priming effects in forests. This knowledge is important because it advances our understanding on the microbial mechanisms mediating soil-climate feedbacks at a continental scale.

Microbial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite Composition

Rapid microbial growth in the early phase of plant litter decomposition is viewed as an important component of soil organic matter (SOM) formation. However, the microbial taxa and chemical substrates that correlate with carbon storage are not well resolved. The complexity of microbial communities and diverse substrate chemistries that occur in natural soils make it difficult to identify links between community membership and decomposition processes in the soil environment. To identify potential relationships between microbes, soil organic matter, and their impact on carbon storage, we used sand microcosms to control for external environmental factors such as changes in temperature and moisture as well as the variability in available carbon that exist in soil cores. Using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) on microcosm samples from early phase litter decomposition, we found that protein- and tannin-like compounds exhibited the strongest correlation to dissolved organic carbon (DOC) concentration. Proteins correlated positively with DOC concentration, while tannins correlated negatively with DOC. Through random forest, neural network, and indicator species analyses, we identified 42 bacterial and 9 fungal taxa associated with DOC concentration. The majority of bacterial taxa (26 out of 42 taxa) belonged to the phylum Proteobacteria while all fungal taxa belonged to the phylum Ascomycota. Additionally, we identified significant connections between microorganisms and protein-like compounds and found that most taxa (12/14) correlated negatively with proteins indicating that microbial consumption of proteins is likely a significant driver of DOC concentration. This research links DOC concentration with microbial production and/or decomposition of specific metabolites to improve our understanding of microbial metabolism and carbon persistence.

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.

Rhizosphere soil properties, microbial community, and enzyme activities: Short-term responses to partial substitution of chemical fertilizer with organic manure

The partial substitution of chemical fertilizers with organic manure has positive effects on crop productivity and sustainable development. Nevertheless, few studies have focused on major grain crops. Herein, we report the short-term effects of the partial substitution of chemical fertilizers with organic manure on the physicochemical properties, microbial community, and enzyme activities in the rhizosphere soil of a maize (Zea mays L.) field. A decrease in soil bulk density, pH, and electrical conductivity, concomitant with an increase in soil urease, invertase, and alkaline phosphatase activities, and a high level of nutrients were observed in organic manure-treated soil. The influence of the organic substitution treatment on bacterial diversity was greater than that on fungal diversity, particularly on alpha diversity. Among dominant bacterial phyla, Actinobacteria abundance changed the most, with significantly increase under organic manure treatment. In turn, among fungi, only Ascomycota responded substantially to organic substitution. Binding spatial ordination analysis revealed that relative soil water content and soil organic carbon, and nitrate and total nitrogen contents had a stronger effect on bacteria and fungi, respectively, than any other soil physicochemical property. Additionally, the changes in bacterial and fungal communities influenced soil enzymatic activities. Moreover, partial least squares path model revealed that soil physicochemical properties indirectly affected soil enzymatic activities by their direct effects on microbial (both bacteria and fungi) community. Overall, our results indicate that the substitution of chemical fertilizers by organic manure changed the composition of the soil microbial community, and that the effects of the substitution were more significant on bacteria than on fungi.

Patterns and Internal Stability of Carbon, Nitrogen, and Phosphorus in Soils and Soil Microbial Biomass in Terrestrial Ecosystems in China: A Data Synthesis

Inspired by the strict constraint ratio (relatively low variability) between carbon (C), nitrogen (N), and phosphorus (P) in global soils and soil microbial biomass, our study explores the biogeographic distribution of C:N:P stoichiometric ratios in soils and soil microbial biomass in China and seeks to identify areas with similar ratios. Our study also attempts to determine the impacts of soil and soil microbial biomass C:N:P in China and the factors determining the ratio. The element concentrations may vary in each phylogenetic group of soils and soil microbial communities in China’s terrestrial ecosystems, as they do in global terrestrial ecosystems. However, on average, the C:N:P ratios for soil (66:5:1) and soil microbial biomass (22:2:1) are highly constrained within China. Soil microbial biomass C, N, and P concentrations have relatively weak internal stability, while soil microbial biomass C:N, C:P, and N:P ratios do not have internal stability at the national scale and in different terrestrial ecosystems of China. Unlike plant N:P, which can be used as the basis for evaluations of nutrient restrictions, the use of soil or soil microbial biomass N:P to evaluate soil nutrients is not universal. Latitude is the main factor influencing the patterns of soil C, N, and P. Longitude is the main factor determining the patterns of soil microbial biomass C, N, and P. pH is the main nonzonal factor affecting the patterns of soil and soil microbial biomass C, N, and P. The findings of this study are helpful in understanding the spatial pattern of soils and soil microbial biomass and their influencing factors in regions with complex ecosystems.

K-strategy species plays a pivotal role in the natural attenuation of petroleum hydrocarbon pollution in aquifers

The natural attenuation of petroleum hydrocarbons is inseparable from the action of microorganisms, while the degradation methods and ecological strategies of microorganisms in petroleum-contaminated aquifers are still under debate. In the present study, 16 S rRNA sequencing and quantitative real-time polymerase chain reaction were used to assess the potential microbial degradation of petroleum hydrocarbons, and the ecological strategy of microorganisms under petroleum stress was analyzed through a co-occurrence network. The results showed that the microbial community in sediments exhibit higher efficiency and stability and stronger ecological function than that in groundwater. Keystone species coordinated with the community to execute ecosystem processes and tended to choose a K-strategy to survive, with the aquifer sediment being the main site of petroleum hydrocarbon degradation. Under natural conditions, the presence of petroleum hydrocarbons at concentrations higher than 126 μg kg^-1 and 5557 μg kg^-1 was not conducive to the microbial degradation of polycyclic aromatic hydrocarbons and alkanes, respectively. These results can be used as a reference for an enhanced bioremediation of contaminated groundwater. Overall, these findings provide support to managers for developing environmental management strategies.

The Response of Critical Microbial Taxa to Litter Micro-Nutrients and Macro-Chemistry Determined the Agricultural Soil Priming Intensity After Afforestation

Afforestation with trees and shrubs around cropland can effectively decrease soil degradation and avoid sand storms, but subsequent modification of litter quality accelerates the degradation of native organic matter via the soil priming effect (PE). Although carbon accumulation in agricultural soils after afforestation was widely studied, little is known about the extent to which soil organic carbon (SOC) mineralization is induced by complex residue input in agro-forest-grass composite ecosystems. Here, we mixed corn field soil and litter of afforestation tree and shrub species together in a micro-environment to quantify the effects of litter-mixture input on farmland soil priming associated with afforestation. Additionally, we studied the responses of bacterial and fungal species to litter chemistry, with the aim to identify the litter and microbial driver of soil priming. The results showed that soil priming was accelerated by different litter addition which varied from 24 to 74% of SOC mineralization, suggesting that priming intensity was relatively flexible and highly affected by litter quality. We also find that the macro-chemistry (including litter carbon, nitrogen, lignin, and cellulose) directly affects priming intensity, while micro-chemistry (including litter soluble sugar, water-soluble phenol, methanol-soluble phenol, and condensed tannin) indirectly influences priming via alteration to dominant bacterial taxa. The stepwise regression analysis suggested that litter nitrogen and cellulose were the critical litter drivers to soil priming (r 2 = 0.279), and the combination of bacterial phylum Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and fungal taxa Eurotiomycetes was a great model to explain the priming intensity (r 2 = 0.407).

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

Artificial Plantation Responses to Periodic Submergence in Massive Dam and Reservoir Riparian Zones: Changes in Soil Properties and Bacterial Community Characteristics

Simple Summary

This study focuses on plants in riparian zones that are very vulnerable due to water stress and anthropogenic disturbances, which are particularly important regarding their ecological and environmental role. Although plants and microbiome interactions are necessary for plant nutrient acquisition, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities of different artificial vegetation types in riparian areas of massive dams and reservoirs. Therefore, this study aims to assess the responses of woody and herbaceous plants in the riparian zones of the Three Gorges Dam Reservoir, China. Results revealed that the weight of dominant soil bacteria in different periods, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Cyanobacteria, was higher, and their composition was different in the rhizosphere, bulk soil, and endophyte. In the soil co-occurrence networks, the weight of soil physical properties was higher than chemical properties in the early emergence stage. The current study provides knowledge about bacteria in bulk, rhizosphere soils, and within roots in different emergence phases. Additionally, these results provide valuable information to inoculate the soil with key microbiota members by applying fertilizers, potentially improving plant and soil production and health.

Abstract

Plant and microbiome interactions are necessary for plant nutrient acquisition. However, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities in different artificial vegetation types (woody and herbaceous) in riparian areas of massive dams and reservoirs. Therefore, this study aims to assess such responses at elevations of 165–170 m a.s.l. in the riparian zones of the Three Gorges Dam Reservoir, China. The samples were collected containing the rhizosphere soil, bulk soil, and roots of herbaceous and woody vegetation at different emergence stages in 2018. Then, all the samples were analyzed to quantify the soil properties, bacterial community characteristics, and their interaction in the early and late emergence phases. In different periods, the weight of dominant soil bacteria, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Cyanobacteria, was higher, and their composition was different in the rhizosphere, bulk soil, and endophytes. Moreover, the soil co-occurrence networks indicated that the weight of soil physical properties was higher than chemical properties in the early emergence stage. In contrast, the weight of chemical properties was relatively higher in the late emergence stage. Furthermore, the richness and diversity of the bacterial community were mainly affected by soil organic matter. This study suggests that these herbaceous and woody vegetation are suitable for planting in reservoir areas affected by hydrology and human disturbance in light of soil nutrients and soil microbial communities, respectively. Additionally, these results provide valuable information to inoculate the soil with key microbiota members by applying fertilizers, potentially improving plant health and soil production.

Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome

Recruitment of microorganisms to the rhizosphere varies among plant genotypes, yet an understanding of whether the microbiome can be altered by selection on the host is relatively unknown. Here, we performed a common garden study to characterize recruitment of rhizosphere microbiome, functional groups, for 20 expired Plant Variety Protection Act maize lines spanning a chronosequence of development from 1949 to 1986. This time frame brackets a series of agronomic innovations, namely improvements in breeding and the application of synthetic nitrogenous fertilizers, technologies that define modern industrial agriculture. We assessed the impact of chronological agronomic improvements on recruitment of the rhizosphere microbiome in maize, with emphasis on nitrogen cycling functional groups. In addition, we quantified the microbial genes involved in nitrogen cycling and predicted functional pathways present in the microbiome of each genotype. Both genetic relatednesses of host plant and decade of germplasm development were significant factors in the recruitment of the rhizosphere microbiome. More recently developed germplasm recruited fewer microbial taxa with the genetic capability for sustainable nitrogen provisioning and larger populations of microorganisms that contribute to N losses. This study indicates that the development of high-yielding varieties and agronomic management approaches of industrial agriculture inadvertently modified interactions between maize and its microbiome.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Above- and belowground biodiversity drives soil multifunctionality along a long-term grassland restoration chronosequence

Restoring degraded land is an efficient strategy for improving biodiversity and ecosystem functioning. However, the effects of aboveground and belowground biodiversity on multiple ecosystem functions (multifunctionality) during ecological restoration are not well understood. Here, the relationships between plant and microbial communities and soil multifunctionality were assessed in a 30-year natural grassland restoration chronosequence on the Loess Plateau, China. Soil multifunctionality, in relation to the carbon, nitrogen, phosphorus, and sulfur cycles, was quantified. Soil bacterial and fungal communities were analyzed by high-throughput sequencing using the Illumina HiSeq platform. The results showed that soil multifunctionality was significantly increased with the increasing period of grassland restoration. Plant and bacterial diversity, rather than fungal diversity, were significantly and positively correlated with soil multifunctionality based on single functions, averaging, and multiple threshold approaches. Random forest and structural equation modeling analyses showed that soil multifunctionality was affected by both biotic and abiotic factors. Plant diversity and bacterial community composition had direct effects, whereas plant community composition had both direct and indirect effects on soil multifunctionality. Restoration period and soil pH indirectly affected soil multifunctionality by altering plant and bacterial communities. This work demonstrates the importance of aboveground and belowground biodiversity in driving soil multifunctionality during grassland restoration. The results provide empirical evidence that conserving biodiversity is crucial for maintaining ecosystem functions in restored areas.

Crops for Carbon Farming

Agricultural cropping systems and pasture comprise one third of the world's arable land and have the potential to draw down a considerable amount of atmospheric CO2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.

Temperature sensitivity of SOM decomposition is linked with a K-selected microbial community

Temperature sensitivity (Q₁₀ ) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q₁₀ to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q₁₀ , SOM quality, and soil microorganisms. We examined the Q₁₀ of SOM decomposition across a mean annual temperature (MAT) gradient from -1.9 to 5.1°C in temperate mixed forest ecosystems in parallel with SOM quality and bioavailability, microbial taxonomic composition, and functional genes responsible for organic carbon decomposition. Within this temperature gradient of 7.0°C, the Q₁₀ values increased with MAT, but decreased with SOM bioavailability. The Q₁₀ values increased with the prevalence of K-strategy of soil microbial community, which was characterized by: (i) high ratios of oligotrophic to copiotrophic taxa, (ii) ectomycorrhizal to saprotrophic fungi, (iii) functional genes responsible for degradation of recalcitrant to that of labile C, and (iv) low average 16S rRNA operon copy number. Because the recalcitrant organic matter was mainly utilized by the K-strategists, these findings independently support the carbon quality-temperature theory from the perspective of microbial taxonomic composition and functions. A year-long incubation experiment was performed to determine the response of labile and recalcitrant C pools to warming based on the two-pool model. The decomposition of recalcitrant SOM was more sensitive to increased temperature in southern warm regions, which might attribute to the dominance of K-selected microbial communities. It implies that climate warming would mobilize the larger recalcitrant pools in warm regions, exacerbating the positive feedback between increased MAT and CO₂ efflux. This is the first attempt to link temperature sensitivity of SOM decomposition with microbial eco-strategies by incorporating the genetic information and disentangling the complex relationship between Q₁₀ and soil microorganisms.

Functional trait relationships demonstrate life strategies in terrestrial prokaryotes

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils

BACKGROUND

Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria, one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with 13C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition.

RESULTS

While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and 13C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility.

CONCLUSIONS

This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling. Video abstract.

Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world

Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.

Life-history strategies of soil microbial communities in an arid ecosystem

The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.

The sum is greater than the parts: exploiting microbial communities to achieve complex functions

Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.

Co-application of a biosolids product and biochar to two coarse-textured pasture soils influenced microbial N cycling genes and potential for N leaching

Co-application of biochar and biosolids to soil has potential to mitigate N leaching due to physical and chemical properties of biochar. Changes in N cycling pathways in soil induced by co-application of biological amendments could further mitigate N loss, but this is largely unexplored. The aim of this study was to determine whether co-application of a biochar and a modified biosolids product to three pasture soils differing in texture could alter the relative abundance of N cycling genes in soil sown with subterranean clover. The biosolids product contained lime and clay and increased subterranean clover shoot biomass in parallel with increases in soil pH and soil nitrate. Its co-application with biochar similarly increased plant growth and soil pH with a marked reduction in nitrate in two coarse textured soils but not in a clayey soil. While application of the biosolids product altered in silico predicted N cycling functional genes, there was no additional change when applied to soil in combination with biochar. This supports the conclusion that co-application of the biochar and biosolids product used here has potential to mitigate loss of N in coarse textured soils due to N adsoption by the biochar and independently of microbial N pathways.

Metagenomics for taxonomy profiling: tools and approaches

The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.