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Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation
Abstract
The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.
... The Karst Mountains of Southwestern China, spanning approximately 540,000 km 2 , represent one of the most extensive continuous karst landscapes globally [1]. This region has experienced profound losses in agricultural and forestry productivity, alongside drastic declines in plant diversity, soil physicochemical characteristics, microbial diversity, and carbon sequestration capacity [2][3][4]. These changes are attributed to a variety of natural and human-induced disturbances, rendering it one of the areas most severely impacted by rocky desertification [5]. ...
This study investigates the role of abscisic acid (ABA) in bolstering drought resistance in plants, employing “Panjiang Sophora viciifolia” as the subject. A simulated drought scenario was created using polyethylene glycol (PEG-6000) to examine the impact of varying drought intensities (0%, 5%, 20% PEG) and ABA concentrations (0, 10, 50, 100, 200 mg·L−1) on the germination and physiological parameters of Sophora viciifolia. The results showed that in the absence of ABA, the germination rate (GR), germination potential (GP), and germination index (GI) of S. viciifolia seeds initially increased and then decreased with escalating PEG-induced drought stress. At PEG-induced drought stress levels of 5% and 20%, the activities of peroxidase (POD) and catalase (CAT), along with the malondialdehyde (MDA) content, were significantly higher than in the control (CK) (p < 0.05). In response to drought stress, S. viciifolia seeds adapted by modulating germination behavior, augmenting the content of osmoregulatory substances, and boosting the activity of protective enzymes. The addition of ABA markedly enhanced GR, GE, GI, activities of POD, superoxide dismutase (SOD), and CAT, as well as the levels of MDA and proline (Pro) under drought conditions (p < 0.05). Relative to CK, low ABA concentrations (10–100 mg·L−1) resulted in increased GR, GP, GI, POD, SOD, CAT, MDA, and Pro levels; whereas, at a higher concentration (200 mg·L−1), although GR, GP, and GI decreased, POD, SOD, CAT, MDA, and Pro levels increased. Through principal component analysis and membership function comprehensive evaluation, it was determined that administering 50 mg·L−1 ABA was most effective in enhancing drought resistance in S. viciifolia seedlings.
Bacteria, fungi, and protists occupy a pivotal position in maintaining soil ecology. Despite limited knowledge on their responses to managed vegetation restoration strategies in karst regions, we aimed to study the essential microbial communities involved in the process of vegetation restoration. We compared microbial characteristics in four land use types: planted forests (PF), forage grass (FG), a mixture of plantation forest and forage grass (FF), and cropland (CR) as a reference. Our findings revealed that the richness of bacteria and protists was higher in FF compared to PF, while fungal richness was lower in both PF and FF than in CR. Additionally, the bacterial Shannon index in FF was higher than that in CR and PF, while the fungal and protist Shannon indices were similar across all four land use types. Significant differences were observed in the compositions of bacterial, fungal, and protist communities between FF and the other three land use types, whereas bacterial, fungal, and protist communities were relatively similar in PF and FG. In FF, the relative abundance of bacterial taxa Acidobacteria, Firmicutes, and Gemmatimonadetes was significantly higher than in PF and CR. Fungal communities were dominated by Ascomycota and Basidiomycota, with the relative abundance of Ascomycota significantly higher in FF compared to other land use types. Regarding protistan taxa, the relative abundance of Chlorophyta was higher in FF compared to CR, PF, and FG, while the relative abundance of Apicomplexa was higher in CR compared to FF. Importantly, ammonium nitrogen, total phosphorus, and microbial biomass nitrogen were identified as key soil properties predicting changes in the diversity of bacteria, fungi, and protists. Our results suggest that the microbial community under FF exhibits greater sensitivity to vegetation restoration compared to PF and FG. This sensitivity may stem from differences in soil properties, the formation of biological crusts and root systems, and management activities, resulting in variations in bacterial, fungal, and protist diversity and taxa in PF. As a result, employing a combination restoration strategy involving plantation forest and forage grass proves to be an effective approach to enhance the microbial community and thereby improve ecosystem functionality in ecologically fragile areas.
The various vegetation types in the karst landscape have been considered the results of heterogeneous habitats. However, the lack of a comprehensive understanding of regional biodiversity patterns and the underlying ecological processes limits further research on ecological management. This study established forest dynamic plots (FDPs) of the dominant vegetation types (shrubland, SL; mixed tree and shrub forest, MTSF; coniferous forest, CF; coniferous broadleaf mixed forest, CBMF; and broadleaf forest, BF) in the karst landscape and quantified the species diversity patterns and potential ecological processes. The results showed that in terms of diversity patterns, the evenness and species richness of the CF community were significantly lower than other vegetation types, while the BF community had the highest species richness. The other three vegetation types showed no significant variation in species richness and evenness. However, when controlling the number of individuals of FDPs, the rarefied species richness showed significant differences and ranked as BF > SL > MTSF > CBMF > CF, highlighting the importance of considering the impacts of abundance. Additionally, the community assembly of climax communities (CF or BF) was dominated by stochastic processes such as species dispersal or species formation, whereas deterministic processes (habitat filtering) dominated the secondary forests (SL, MTSF, and CBMF). These findings proved that community assembly differs mainly between the climax community and other communities. Hence, it is crucial to consider the biodiversity and of the potential underlying ecological processes together when studying regional ecology and management, particularly in heterogeneous ecosystems.
Aims:
Soil phosphorus (P) cycling in karst regions is mainly regulated by microbial activities. Natural restoration has been widely adopted in the degraded karst regions of southwest China. However, the response of functional genes and microbial communities involved in soil P cycling to revegetation has not been well characterized.
Methods:
We used metagenomic sequencing to investigate the genes and microorganisms related to soil P cycling derived from natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China.
Results:
Natural restoration affected the composition of soil P cycling genes. When TG restored into OG, the relative abundance of organic P (OP) mineralization genes increased from 45.78% to 48.38%, while the genes related to inorganic P (IP) solubilization decreased from 27.19% to 25.03%. The effect of soil nutrients on the relative abundance of OP and IP genes was greater than that of aboveground plant diversity. Structural equation modeling further indicated that soil nutrients directly drove the increase in the relative abundance of OP genes and indirectly impacted the relative abundance of IP genes. The results show that Proteobacteria (38.97%–52.72%) and Actinobacteria (13.44%–29.34%) are the main contributors to soil OP and IP cycling genes, but their contributions vary in different restoration stages.
Conclusions:
Natural restoration of the degraded karst vegetation changes the acquisition strategy of soil microbial P by enhancing OP but decreasing IP cycling potentials. This study investigate the regulation of P cycling in the ecological restoration of degraded karst regions from microbial perspective.
BackgroundsA large-scale ecological restoration project was initiated in the 1990s in southwest China, which is one of the largest areas of rocky desertification globally. However, the influence and potential mechanisms of vegetation restoration on soil carbon(C) sequestration in karst and non-karst regions remains unclear.Methods
Based on field investigation and multi-source data synthesis, the mechanisms of soil C sequestration were investigated to determine the most important variables affecting the rate of soil C change (Rs) in southwest China.ResultsOur results show significant differences in soil C sequestration between karst and non-karst regions with faster and longer C sequestration occurring in karst regions. In these areas, Rs was approximately 31% higher than in non-karst soils. The Rs of shrubland, grassland and cropland sites in karst areas was significantly higher than that observed in non-karst areas. We found that temperatures were the primary factor inhibiting soil C sequestration instead of precipitation. The total effect of nitrogen (N) on Rs was positive in both karst and non-karst regions.Conclusions
Phosphorus was the dominant factor limiting the use of N by vegetation in karst regions and then resulting in limitation of C sequestration. The results indicated that soil C storage may increase intermittently due to combination of karst environment and climate change in southwest China in future.
Understanding the driving factors of soil multifunctionality is of great significance for the protection and restoration of degraded terrestrial ecosystems. However, the effects of above- and belowground factors are rarely evaluated simultaneously, and the driving mode of both factors on soil multifunctionality is not clear. Here, we evaluated restoration of mobile dunes threatened by desertification through aerial seeding, i.e., the sowing of seeds through aerial devices, from 1983 to 2015 in Mu Us Desert, China, using soil and plant data. The effect of aerial seeding on the restoration of soil multifunctionality, plant diversity, and soil microbial diversity in mobile dunes was significant, which tested by loess regression. Further, the plant diversity becomes saturated in the later stages of restoration. The effect also leads to the restoration of soil multifunctionality lags behind plant and soil microorganisms. The factors (plant and soil microorganisms) driving soil multifunctionality is not a separate action or a joint action which test by structural equation models (SEMs), but that plants restore first and then indirectly drive soil multifunctionality through soil microorganisms during the restoration process. We also found that bacteria are the main direct indicators of soil multifunctionality which tested using Random Forests modelling. This study highlights that plants indirectly drive soil multifunctionality through soil microorganisms, and soil microorganisms are key to elucidating the restoration mechanism and process.
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BackgroundsVegetation dynamics play a dominant role in the global carbon cycle and climate, especially in vulnerable karst ecosystem. Many studies have examined the past several decades changes in vegetation greenness and the associated with climate drivers. Yet, few studies have analyzed the vegetation change in global karst regions particularly in the last decades when climate change and anthropogenic disturbance widely occurred.Methods
In this study, we investigated the spatio-temporal variations in vegetation dynamic using the Seasonally Integrated Normalized Difference Vegetation Index (SINDVI) and examined their relationship with climate changes using correlation analysis, the ordinary least squares method investigate the variation trends and the Mann-Kendal test to detect the turning points from 2001 to 2020.ResultsAs expected, there were greening trends in global karst SINDVI from 2001 to 2020, with significant increasing trends in China (range = 0.836, P < 0.05), Europe (range = 0.456, P < 0.05) and many other regions. According to correlation analyses, SINDVI was water-limited in arid and semi-arid regions, such as Middle East and central Asia, and temperature-limited in northern high-latitude.Conclusions
Our results suggest that anthropogenic activities were mainly responsible for the increasing vegetation greenness in tailoring management measures (e.g., Ecological Engineering, the Grain to Green Project) in China and Europe, and intensive farm in Middle East. Coupling warming temperature and increasing precipitation, southeastern Asia and Russia showed increasing trends in SINDVI. In general, climate factors were the dominant drivers for the variation in vegetation greenness in globally karst regions during research period.
Aims
We explored the trends in soil fungal and bacterial patterns and their responses to plant and soil characteristics with increasing site age in abandoned farmland in karst areas.
Methods
Illumina sequencing of 16S rRNA and ITS genes was used to characterize the soil bacterial and fungal diversities in farmland, farmland abandoned for 3, 6, 20, and 40 years, and old-growth forests in Southwest China. Plant diversity, community-weighted mean (CWM) leaf and branch traits, soil physical and chemical properties and metal element concentrations were also investigated.
Results
Bacterial diversity decreased slightly with increasing site age, while fungal diversity first increased and then decreased. Ascomycota was the dominant fungal phylum, and its abundance decreased significantly, from 83.21% in farmland to 49.66% in old-growth forests, while that of Basidiomycota increased significantly from 4.52 to 35.43%. The soil bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi. The fungal and bacterial diversities were mainly affected by soil properties. At the older sites, high levels of soil nitrate nitrogen (N), ammonium-N, total N, soil organic carbon, calcium, and magnesium and relatively low levels of soil potassium and available phosphorus (P) resulted in decreased bacterial diversity. Fungal diversity was positively affected by soil total P and pH and negatively affected by soil iron and copper. The bacterial and fungal compositions were jointly affected by soil properties and CWM leaf and branch traits.
Conclusions
Our findings indicate that soil bacterial and fungal diversities and compositions changed significantly during secondary succession in karst areas. Microbial diversity was determined by soil properties, and compositions were jointly driven by plant and soil properties.
Background and aimsKarst rocky desertification (KRD) influences soil properties and plant species. Soil microbes are important factors in maintaining ecosystem stability. However, little is known about the role of fungi in adaptation of plants to KRD.Methods
Fungi colonized in bulk soil, rhizosphere, and roots of Themeda japonica at strong and slight KRD were analyzed by ITS2 amplicon sequencing. The relationship between soil nutrients and fungal diversity was estimated by redundancy analysis (RDA) and Spearman analysis.ResultsAN, NN, SOC, TN, TP content and pH in strong KRD soil were higher than those with slight KRD. Rhizosphere with slight KRD had higher fungal richness and diversity than it with strong KRD, but there was no difference in root endophyte between KRD grades. The bulk soil with slight KRD had higher fungal richness compare to strong KRD. The fungal communities in bulk soil, rhizosphere, and root between plants at different KRD grades were significantly different. In addition, the fungal communities of rhizosphere were sensitive to the change of KRD environment. Ascomycota and Basidiomycota were the predominant phyla in bulk soil, rhizosphere and root endophyte at strong and slight KRD. SOC, AN and pH influenced the composition of fungal communities at strong KRD. In contrast, TN and AN had a negative impact on richness.Conclusion
Our results suggest that fungal communities of rhizosphere may play a role in adaptation of T. japonica to KRD and may contribute to promote plant growth and ecological performance in karst areas.
We are at the beginning of a genomic revolution in which all known species are planned to be sequenced. Accessing such data for comparative analyses is crucial in this new age of data-driven biology. Here, we introduce an improved version of DIAMOND that greatly exceeds previous search performances and harnesses supercomputing to perform tree-of-life scale protein alignments in hours, while matching the sensitivity of the gold standard BLASTP. An updated version of DIAMOND uses improved algorithmic procedures and a customized high-performance computing framework to make seemingly prohibitive large-scale protein sequence alignments feasible.
Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.
Aims
This study aimed to determine the responses of soil bacteria and fungi to plant species diversity and plant family composition (PFC) following secondary succession on former farmland (FL).
Methods
Illumina sequencing of 16S rRNA and ITS genes was used to determine soil microbial communities along a chronosequence of FL left abandoned for 0, 10, 20, 30, 40, and 50 years on the Loess Plateau. Soil properties, plant diversity, and PFC were also investigated.
Results
Fungal communities were dominated by Ascomycota and Basidiomycota. Fungal diversity and Ascomycota abundance increased with time, while Basidiomycota abundance decreased. The fungal diversity and dominant phyla were related to the increasing levels of plant species diversity and evenness with succession. Bacterial diversity first increased and then decreased as succession proceeded, peaking at 30 years. Bacterial communities transitioned from Actinobacteria to Proteobacteria dominance during the first 30 years, after which Actinobacteria was dominant. Plant family composition exerted indirect effects on the diversity and dominant phyla of bacterial communities, mainly through direct effects on soil organic carbon and total nitrogen content. Bacterial diversity and Proteobacteria abundance were higher at Leguminosae- and Gramineae-dominant succession stages, but lower in Compositae-dominant plots; Actinobacteria showed the opposite result.
Conclusions
Plant species diversity and evenness might be the key drivers for shaping fungal communities, but bacteria are influenced more by changes in PFC and abiotic soil nutrient levels during succession.
Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO2 concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long‐term predictions of climate C‐feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta‐analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long‐term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short‐term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long‐term climate‐C feedbacks.
Soil organic matter (SOM) is the dominant reservoir of terrestrial organic carbon and nitrogen, and microbial necromass represents a primary input to it. However, knowledge of stabilization mechanisms and direct measurements of the decomposition of microbial-derived SOM are lacking. Here we report a novel ¹⁵N isotope pool dilution approach using labeled amino sugars and muropeptides as tracers to quantify the decomposition of proteins and microbial cell walls, which allows to estimate in situ decomposition rates of microbial-derived SOM. Our results demonstrate that microbial cell walls are as recalcitrant as soil protein, exhibiting comparable turnover times across various ecosystems. The bacterial peptidoglycan in soils was primarily decomposed to muropeptides which can be directly utilized by microbes without being further depolymerized to free amino compounds. Moreover, bacterial peptidoglycan decomposition was correlated with soil microbial biomass while fungal chitin and soil protein decomposition were correlated with high soil pH and fine soil texture. This approach thereby provides new insights into the decomposition pathways and stabilization mechanisms of microbial-derived SOM constituents pertaining to SOM persistence.
Soil carbon transformation and sequestration have received significant interest in recent years due to a growing need for quantifying its role in mitigating climate change. Even though our understanding of the nature of soil organic matter has recently been substantially revised, fundamental uncertainty remains about the quantitative importance of microbial necromass as part of persistent organic matter. Addressing this uncertainty has been hampered by the absence of quantitative assessments whether microbial matter makes up the majority of the persistent carbon in soil. Direct quantification of microbial necromass in soil is very challenging because of overlapping molecular signature with non‐microbial organic carbon. Here we use a comprehensive analysis of existing biomarker amino sugar data published between 1996‐2018, combined with novel appropriation using ecological systems approach, elemental carbon‐nitrogen stoichiometry, and biomarker scaling, to demonstrate a suit of strategies for quantifying the contribution of microbe‐derived carbon to the topsoil organic carbon reservoir in global temperate agricultural, grassland, and forest ecosystems. We show that microbial necromass can make up more than half of soil organic carbon. Hence, we suggest next‐generation field management requires promoting microbial biomass formation and necromass preservation to maintain healthy soils, ecosystems, and climate. Our analyses have important implications for improving current climate and carbon models, and helping develop management practices and policies. This article is protected by copyright. All rights reserved.
Understanding how patterns of recovery and geological conditions affect microbial communities is important for determining the stability of karst ecosystems. Here, we investigated the diversity and composition of microorganisms in karst and non-karst environments under natural restoration and artificial rehabilitation conditions. The results showed no significant differences in soil microbial diversity, but the microbial communities associated with geological conditions and tree species differed significantly. Variation partitioning analysis (VPA) showed that a total of 77.3% of the variation in bacteria and a total of 69.3% of the variation in fungi could be explained by vegetation type and geological background. There were significant differences in six bacterial classes (Actinobacteria, Alphaproteobacteria, Ktedonobacteria, TK10, Gammaproteobacteria, and Anaerolineae) and nine fungal classes (Eurotiomycetes, Agaricomycetes, unclassified _p_Ascomycota, Sordariomycetes, Tremellomycetes, norank_k_Fungi, Pezizomycetes, Leotiomycetes and Archaeorhizomycetes) among the soils collected from six plots. A Spearman correlation heatmap showed that the microbial community was affected by the major soil properties. Principal coordinates analysis indicated that the microbial community of Pinus yunnanensis in the artificial forest, which was established for the protection of the environment was most similar to that in the natural secondary forest in the karst ecosystem. These findings further our understanding of microbial responses to vegetation restoration and geological conditions.
Motivation
Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.
Results
We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.
Availability and implementation
The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
Extracellular enzymes catalyze rate‐limiting steps in soil organic matter decomposition, and their activities (EEAs) play a key role in determining soil respiration (SR). Both EEAs and SR are highly sensitive to temperature, but their responses to climate warming remain poorly understood. Here, we present a meta‐analysis on the response of soil cellulase and ligninase activities and SR to warming, synthesizing data from 56 studies. We found that warming significantly enhanced ligninase activity by 21.4% but had no effect on cellulase activity. Increases in ligninase activity were positively correlated with changes in SR, while no such relationship was found for cellulase. The warming response of ligninase activity was more closely related to the responses of SR than a wide range of environmental and experimental methodological factors. Furthermore, warming effects on ligninase activity increased with experiment duration. These results suggest that soil microorganisms sustain long term increases in SR with warming by gradually increasing the degradation of the recalcitrant carbon pool.
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Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database. Combining the three outputs and removing CAZymes found by only one tool can significantly improve the CAZome annotation accuracy. In addition, dbCAN2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked CAZyme gene clusters (CGCs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (PULs) in microbial genomes or metagenomes.
Long‐term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long‐term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long‐term N and NPK fertilization on soil bacterial diversity and community composition using meta‐analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity was positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long‐term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long‐term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro‐ecosystems worldwide.
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The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.
Afforestation and reforestation projects in the karst regions of southwest China aim to combat desertification and improve the ecological environment. However, it remains unclear at what scale conservation efforts have impacted on carbon stocks and if vegetation regrowth occurs at a large spatial scale as intended. Here we use satellite time series data and show a widespread increase in leaf area index (a proxy for green vegetation cover), and aboveground biomass carbon, which contrasted negative trends found in the absence of anthropogenic influence as simulated by an ecosystem model. In spite of drought conditions, aboveground biomass carbon increased by 9% (+0.05 Pg C y−1), mainly in areas of high conservation effort. We conclude that large scale conservation projects can contribute to a greening Earth with positive effects on carbon sequestration to mitigate climate change. At the regional scale, such ecological engineering projects may reduce risks of desertification by increasing the vegetation cover and reducing the ecosystem sensitivity to climate perturbations. Since 2000, China has attempted to vegetate huge portions of eroded landscape in its south west, bordering Vietman, Laos, and Myanmar. This study finds that this ecological engineering is combating desertification as vegetation regrows and stores carbon.
We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.
Vegetation restoration has been widely used in karst rocky desertification (KRD) areas of southwestern China, but the response of microbial community to revegetation has not been well characterized. We investigated the diversity, structure, and co-occurrence patterns of bacterial communities in soils of five vegetation types (grassland, shrubbery, secondary forest, pure plantation and mixed plantation) in KRD area using high-throughput sequencing of the 16S rRNA gene. Bray-Curtis dissimilarity analysis revealed that 15 bacterial community samples were clustered into five groups that corresponded very well to the five vegetation types. Shannon diversity was positively correlated with pH and Ca2+ content but negatively correlated with organic carbon, total nitrogen, and soil moisture. Redundancy analysis indicated that soil pH, Ca2+ content, organic carbon, total nitrogen, and soil moisture jointly influenced bacterial community structure. Co-occurrence network analysis revealed nonrandom assembly patterns of bacterial composition in the soils. Bryobacter, GR-WP33-30, and Rhizomicrobium were identified as keystone genera in co-occurrence network. These results indicate that diverse soil physicochemical properties and potential interactions among taxa during vegetation restoration may jointly affect the bacterial community structure in KRD regions.
The elevational pattern of soil microbial diversity along mountain slopes has received considerable interest over the last decade. An increasing amount of taxonomic data on soil microbial community composition along elevation gradients have been collected, however the trophic patterns and environmental drivers of elevational changes remain largely unclear. Here, we examined the distribution patterns of major soil bacterial and fungal taxa along the northern slope of Changbai Mountain, Northeast China, at five typical vegetation types located between 740 and 2,691 m above sea level. Elevational patterns of the relative abundance of specific microbial taxa could be partially explained by the oligotrophic-copiotrophic theory. Specifically, two dark-coniferous forests, located at mid-elevation sites, were considered to be oligotrophic habitats, with relatively higher soil C/N ratio and NH4+-N concentrations. As expected, oligotrophic microbial taxa, belonging to the bacterial phyla Acidobacteria and Gemmatimonadetes, and fungal phylum Basidiomycota, were predominant in the two dark-coniferous forests, exhibiting a mid-elevation maximum pattern. In contrast, the broad leaf-Korean pine mixed forest located at the foot of the mountain, Betula ermanii-dominated forest located below the tree line, and alpine tundra at the highest elevation were considered more copiotrophic habitats, characterized by higher substrate-induced-respiration rates and NO3--N concentrations. Microbial taxa considered to be so called copiotrophic members, such as bacterial phyla Proteobacteria and Actinobacteria, and fungal phylum Ascomycota, were relatively abundant in these locations, resulting in a mid-elevation minimum pattern. At finer taxonomic levels, the two most abundant proteobacterial classes, alpha- and beta-Proteobacteria, along with Acidobacteria Gp1, 2, 3, 15, and the Basidiomycotal class of Tremellomycetes were classified with the copiotrophic group. Gamma- and delta-Proteobacteria, Acidobacteria Gp4, 6, 7, 16, and Basidiomycotal class of Agaricomycetes were classified as oligotrophic taxa. This work uses the oligotrophic-copiotrophic theory to explain the elevational distribution pattern of the relative abundance of specific microbial taxa, confirming some of the existing trophic classifications of microbial taxa and expanding on the theory to include a broader range of taxonomic levels.
Background
Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process.
Results
Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously.
Conclusions
Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil.
Electronic supplementary material
The online version of this article (10.1186/s40168-017-0340-0) contains supplementary material, which is available to authorized users.
Despite our current understanding of soil C and N interactions, less is known about the response and feedback of C mineralization to soil P availability driven by microorganisms. To better understand these interactions, soils with long-term P-sufficient NPK fertilization (available P: 13.4 mg kg À1) and P-deficient NK fertilization (available P: 0.96 mg kg À1) were incubated with and without glucose. CO 2 emissions were monitored to characterize C mineralization during the incubation. The soil bacterial community structure, quantity and metabolic activity were evaluated using high-throughput sequencing, qPCR and microcalorimetric dynamics. Compared with P-sufficient soils, P-deficient soils had significantly lower basal respiration, but a significantly higher net mineralization of added glucose, probably due to higher energy cost of soil microorganisms. Glucose addition promoted microbial biomass and activity, particularly in P-deficient soils, and this improvement was maintained for at least 70 days. Shifts in bacterial community composition were induced by a predominance of several specific taxonomic groups, all of which were capable of solubilizing P in soils. P-deficiency decreases the retention of exogenous labile C into soil. Adding labile C to P-deficient soils may shift P from relatively unavailable soil-bound pools into microbial biomass pools through pool cycling. Our results indicated negative effects of P-deficiency on soil C retention, as well as positive effects of labile C on soil P availability in arable soils.
Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.
The majority of the Earth’s terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming1, 2, 3, 4. Despite evidence that warming enhances carbon fluxes to and from the soil5, 6, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12–17 per cent of the expected anthropogenic emissions over this period7, 8. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon–climate feedback that could accelerate climate change.
Importance:
The massive carbon stocks currently held in soils have been built up over millennia, and, while numerous lines of evidence indicate climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacterial isolated from plots subject to 20 years of 5°C warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.
In the Loess Hilly Region of China, the widespread conversion of cropland to forestland and grassland has resulted in great increased in organic carbon (C), nitrogen (N) and phosphorus (P) stocks in the shallow soil layers. However, knowledge regarding changes in C, N, and P in deep soil is still limited. To elucidate the responses of deep soil C, N, and P stocks and stoichiometry in response to changes in land use, the soil from a 0–200 cm soil profile was collected from the following three typical land use patterns in the heartland of the region: forestland, grassland, and cropland. Compared with cropland, forestland and grassland had improved soil organic carbon (SOC) and total nitrogen (TN) contents and stocks at most soil depths but decreased total phosphorus (TP) contents and stocks. At soil depths of 0–200 cm in the forestland and grassland, the cumulative SOC stocks were improved by 34.97% and 7.61%, respectively, and the TN stocks were improved by 54.54% and 12.47%, respectively. The forestland had higher SOC, TN and TP contents and stocks compared to the grassland in almost all soil layers. The soil depths of 100–200 cm contained the highest percentages of SOC, TN and TP stocks (47.80%–49.93%, 46.08%–50.05% and 49.09%–52.98%, respectively). Additionally, the forestland and grassland showed enhanced soil C:P, N:P and C:N:P ratios, and the forestland had higher C:P, N:P and C:N:P ratios compared to the grassland. Furthermore, the SOC and TN stocks had significant impacts on the soil C:N, C:P and N:P ratios. It was concluded that afforestation was the best choice for soil nutrient restoration of degraded land, and deep soil provided an extremely important resource for evaluating soil C, N and P pools and cycling.
There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.
Soil microbes greatly contribute to the regulating of phosphorus (P) cycling, which plays a significant role in maintaining wetland ecosystem processes and function. The microbial functional diversity of soil P cycling in response to wetland degradation, however, remains largely unknown. We used metagenomic sequencing to investigate the microbial community and genes related to soil P cycling in un-degraded marshes and meadows derived from long-term marsh degradation in the Lalu alpine wetland of the Tibetan Plateau. When the marsh degraded into meadow, organic P (OP) mineralization genes increased while genes related to P–starvation response regulation decreased. Proteobacteria (20.5–74.3%) and Actinobacteria (5.6–59.7%) were the dominant phyla in soils and were also the main contributors (39.7–84.1% in total) to soil P–cycling genes. Soil pH was the primary factor influencing the P-cycling functional genes. Soil pH negatively affected the genes related to the P uptake and transport system and had negative effects on the genes related to P–starvation response regulation, OP mineralization, and inorganic P solubilization. These findings may deepen our understanding of the biogeochemical process of soil OP and may be beneficial for wetland management.
Arbuscular mycorrhizal fungi (AMF) and diazotrophs have the potential for nutrient transfer and biological nitrogen fixation in ecosystems, respectively. However, their response to vegetation restoration remains unclear, especially under varying temperature and precipitation levels in karst ecosystems. This study aimed to understand the effects of three climatic levels within four natural and managed vegetation restoration types on the diversity and community composition of AMF and diazotrophs. The interactive effects of temperature, precipitation, and vegetation types affected AMF diversity, while diazotroph diversity was not affected. Under conditions of natural vegetation restoration, there was an increase in AMF diversity in response to increasing temperature and precipitation. AMF richness was higher in shrubland and mature forest than in cropland when temperatures were over 20 ℃ and precipitation was high. Thus, in terms of diversity, AMF were more responsive to changes in climatic conditions and vegetation recovery than diazotrophs. Both AMF and diazotroph community compositions were affected by temperature and vegetation type. The relative abundances of AMF groups (e.g., Gigaspora, Glomus, and Septoglomus) and diazotroph taxa (e.g., Frankia) increased at temperatures above 18 ℃. The relative abundances of the AMF genus Glomus and the diazotroph genus Bradyrhizobium in shrubland and mature forest were higher than those in cropland, while abundances of the AMF genus Septoglomus and diazotroph genus Anabaena increased in cropland. Network complexity increased with increasing temperature and precipitation between AMF and diazotroph taxa. Glomus and Bradyrhizobium showed the most links with other groups, confirming that the dominant genera perform well in the co-occurrence network. These results suggested high hydrothermal regions resist rapid nutrient decomposition by strengthening the interactions between AMF and diazotrophs, especially between the abundant groups Glomus and Bradyrhizobium. Management to increase AMF and diazotroph abundance during vegetation recovery in high climate level may stimulate nutrient absorption and transport.
Diversity and community composition of soil microorganisms along the elevation climosequences have been widely studied, while the microbial metabolic potential, particularly in regard to carbon (C) cycling, remains unclear. Here, a metagenomic analysis of C related genes along five elevations ranging from 767 to 4190 m at Mount Kilimanjaro was analysed to evaluate the microbial organic C transformation capacities in various ecosystems. The highest gene abundances for decomposition of moderate mineralizable compounds, i.e. carbohydrate esters, chitin and pectin were found at the mid-elevations with hump-shaped pattern, where the genes for decompositions of recalcitrant C (i.e. lignin) and easily mineralizable C (i.e. starch) showed the opposite trend (i.e. U-shaped pattern), due to high soil pH and seasonality in both low and high elevations. Notably, the gene abundances for the decompositions of starch, carbohydrate esters, chitin and lignin had positive relationships with corresponding C compounds, indicating the consistent responses of microbial functional profiles and metabolites to elevation climosequences. Understanding of adaptation of microbial communities, potential function and metabolites to elevation climosequences and their influencing factors provided a new insight for the regulation of terrestrial C storage.
Forest soils represent important terrestrial carbon (C) pools, where C is primarily fixed in plant biomass and then is incorporated in the biomass of fungi and bacteria. Although classical concepts assume that fungi are the main decomposers of the recalcitrant organic matter within plant and microbial biomass, whereas bacteria are considered to mostly utilize simpler compounds, recent studies have shown that fungi and bacteria overlap in substrate utilization. Here, we studied the microbial contribution to the recycling of dead biomass by analyzing the bacterial and fungal communities in soil microcosms supplemented with ¹³C-labeled biomass of plant, fungal, and bacterial origin using a combination of DNA-stable isotope probing and metagenomics. Both fungi and bacteria contributed actively to the degradation of complex components of plant and microbial biomass. Specific families of carbohydrate-active enzymes (CAZyme) were involved in the degradation of each biomass type. Moreover, the analysis of five bacterial metagenome-assembled genomes indicated the key role of some bacterial genera in the degradation of plant biomass (Cytophaga and Asticcacaulis) and microbial biomass (Herminiimonas). The enzymatic systems utilized by bacteria are highly complex and complementary but also highly diverse among taxa. The results confirm the importance of bacteria, in addition to fungi, as decomposers of complex organic matter in forest soils.
Ecosystem functional responses such as soil CO 2 emissions are constrained by microclimate, available carbon (C) substrates and their effects upon microbial activity. In tropical forests, phosphorus (P) is often considered as a limiting factor for plant growth, but it is still not clear whether P constrains microbial CO 2 emissions from soils. In this study, we incubated seven tropical forest soils from Brazil and Puerto Rico with different nutrient addition treatments (no addition, Control; C, nitrogen (N) or P addition only; and combined C, N and P addition (CNP)). Cumulative soil CO 2 emissions were fit with a Gompertz model to estimate potential maximum cumulative soil CO 2 emission ( C m ) and the rate of change of soil C decomposition ( k ). Quantitative polymerase chain reaction (qPCR) was conducted to quantify microbial biomass as bacteria and fungi. Results showed that P addition alone or in combination with C and N enhanced C m , whereas N addition usually reduced C m , and neither N nor P affected microbial biomass. Additions of CNP enhanced k , increased microbial abundances and altered fungal to bacterial ratios towards higher fungal abundance. Additions of CNP, however, tended to reduce C m for most soils when compared to C additions alone, suggesting that microbial growth associated with nutrient additions may have occurred at the expense of C decomposition. Overall, this study demonstrates that soil CO 2 emission is more limited by P than N in tropical forest soils and those effects were stronger in soils low in P.
Highlights
A laboratory incubation study was conducted with nitrogen, phosphorus or carbon addition to tropical forest soils. Soil CO 2 emission was fitted with a Gompertz model and soil microbial abundance was quantified using qPCR. Phosphorus addition increased model parameters C m and soil CO 2 emission, particularly in the Puerto Rico soils. Soil CO 2 emission was more limited by phosphorus than nitrogen in tropical forest soils.
Bacteria belong to the key players in the carbon cycling in forest soils and thus affect the global C balance. Our understanding of bacterial contribution to ecosystem processes relies on the analysis of whole communities. Here we combined strain isolation, genome sequencing and metatranscriptomics to analyse the activity of individual bacterial species in the topsoil of a temperate coniferous forest. Our results show that transcription profiles in litter and soil differ, indicating that bacterial activity is shaped by their habitat. Importantly, transcript pools also significant differ between summer when primary producers are active and winter. We show that Acidobacteria and Bacteroidetes with high metabolic capacity for polysaccharide decomposition in their genomes actively transcribe corresponding genes in situ. The rate of the transcription of ribosomal proteins, a proxy of growth, seasonally differs between these “decomposer” taxa and other “opportunistic” bacteria. While the former grow at similar rates in summer and winter, the latter grow much faster in summer when labile C, delivered by plant roots, is available. This paper demonstrates differences in activity of bacterial guilds as well as the importance of environmental drivers for the activity of individual bacteria.
Grassland afforestation strongly influences the structure and function of soil microorganisms. Yet the mechanisms of how afforestation could simultaneously alter both the soil fungal and bacterial communities and its implications for ecosystem management are poorly understood, especially in nitrogen-limited ecosystems. Using high-throughput sequencing of 16S rRNA and ITS rRNA genes, the present study investigated the changes in soil properties and soil microorganisms after afforestation of natural grasslands with Chinese pine (Pinus tabuliformis)on the Loess Plateau in China. Results showed that soil bacterial diversity had no significant differences among the grassland (GL), forest–grassland transition zone (TZ), and forestland (FL), while soil fungal diversity in the GL was significantly higher than that in the FL and TZ (P < 0.05). The proportion of shared OTUs in the soil bacterial community was higher than that in the soil fungal community among the three land use types. The dominant bacterial phylum shifted from Proteobacteria to Actinobacteria, while the dominant fungal phylum shifted from Ascomycota to Basidiomycota after the GL conversion to the FL. The functional groups of ECM fungi increased significantly while biotrophic fungi decreased significantly after grassland afforestation. Both the soil bacterial and fungal communities in the TZ showed great similarity with those in the FL. In addition, among all examined soil properties, soil nitrogen (N)showed a more significant effect on the soil microbial communities. The reduction of soil N after grassland afforestation resulted in both the structure and function changes in soil microbial communities. Our results demonstrated simultaneously differential changes in the composition and diversity of both soil bacterial and fungal communities after afforestation from grasslands to planted forests.
Natural regeneration and reforestation have been widely adopted to improve the degraded soil and promote ecological services in the karst regions of southwestern China. A better understanding the effects of different vegetation types on soil quality and the nutrient limiting factors is very important for each approach. In this study, a secondary forest (SF) and two plantations, Eucalyptus maideni F. V. Muell. (EM, exotic, deciduous broad-leaved) and Pinus yunnanensis Franch. (PY, native, conifer species), were selected in the karst graben basins of southwest China to explore the soil quality using Total Data Set (TDS) and Minimum Data Set (MDS) methods. The results indicated most soil parameters showed significant differences between the different recovery approaches. The TDS method is more precise than the MDS method, but the MDS method can also adequately represent the TDS method for the evaluation of soil quality with different vegetation restoration schemes. In the MDS method, soil organic carbon, available potassium, ammonium nitrogen, acid phosphatase, microbial metabolic quotient, and the Pielou index of the soil microbes were found to be the most important indicators for assessing soil quality. The pure plantation of PY had a negative effect on the soil quality, causing soil nutrient deficiency, compared to the SF and EM plantation, indicating that natural regeneration may be a more effective approach to the amelioration of soil quality in the karst areas. These findings provide an empirical and theoretical basis for the protection, restoration, and management of forest in the degraded karst areas.
To elucidate the effects of land-use types and afforestation age on litter decomposition, soil nutrient dynamics, and their relationship with substrate quality and soil environmental conditions, soil and litter samples were collected from farmland as well as four afforested land-use types (Robinia pseudoacacia: Rps; Caragana korshinskii: Cko; Pinus tabulaeformis: Pta; and Armeniaca sibirica: Asi), with each land-use type having three succession chronosequences (10, 25, and 40 a) in the Gaoxigou catchment area. These twelve afforested lands were converted from similar farmlands, and litterbag experiments were conducted in each land to determine litter decomposition rate (LDR). In addition, the carbon, nitrogen, and phosphorus contents and stoichiometry in soil and litter, soil properties, and litter biomass were determined. The results showed that soil environmental conditions such as soil water content, bulk density, pH, and temperature improved with afforestation age. Soil nutrient contents were higher in afforested lands and increased with afforestation age. The soil organic carbon (OC), total nitrogen (TN), and total phosphorus (TP) were positively correlated with the litter biomass, soil microbial carbon, and soil water content, but were negatively correlated with the soil bulk density, pH, and temperature. The litter OC, TN, and TP contents were mainly affected by the land-use types without being influenced by afforestation age. LDR is the main litter factor affecting soil nutrients, and is significantly influenced by substrate quality and environmental conditions, especially litter TN and N:P ratio, soil water content, and pH. The annual rates of increase for soil OC and TN during the initial (farmland–10a) and middle (10–25 a) periods were significantly higher than those during the later period (25–40 a) in Rps and Cko, but the Pta forest showed a completely opposite trend, which can be explained by a synchronous change in the LDR driven by the soil water content. In addition, the soil OC, TN, and TP contents were positively correlated with the litter TN, TP, and biomass, but had no correlation with the litter OC. The N:P ratio can be used as an indicator to reveal a tight coupling among soil and litter nutrients. Overall, these results provide evidence that litter decomposition in afforestation systems is linked to soil nutrient dynamics, and is mainly limited by substrate quality and environmental conditions.
Forest soils represent important terrestrial carbon (C) pools where C is primarily fixed in the plant-derived biomass but it flows further through the biomass of fungi and bacteria before it is lost from the ecosystem as CO2 or immobilized in recalcitrant organic matter. Microorganisms are the main drivers of C flow in forests and play critical roles in the C balance through the decomposition of dead biomass of different origins. Here, we track the path of C that enters forest soil by following respiration, microbial biomass production, and C accumulation by individual microbial taxa in soil microcosms upon the addition of 13C-labeled biomass of plant, fungal, and bacterial origin. We demonstrate that both fungi and bacteria are involved in the assimilation and mineralization of C from the major complex sources existing in soil. Decomposer fungi are, however, better suited to utilize plant biomass compounds, whereas the ability to utilize fungal and bacterial biomass is more frequent among bacteria. Due to the ability of microorganisms to recycle microbial biomass, we suggest that the decomposer food web in forest soil displays a network structure with loops between and within individual pools. These results question the present paradigms describing food webs as hierarchical structures with unidirectional flow of C and assumptions about the dominance of fungi in the decomposition of complex organic matter.
Soil microorganisms are clearly a key component of both natural and managed ecosystems. Despite the challenges of surviving in soil, a gram of soil can contain thousands of individual microbial taxa, including viruses and members of all three domains of life. Recent advances in marker gene, genomic and metagenomic analyses have greatly expanded our ability to characterize the soil microbiome and identify the factors that shape soil microbial communities across space and time. However, although most soil microorganisms remain undescribed, we can begin to categorize soil microorganisms on the basis of their ecological strategies. This is an approach that should prove fruitful for leveraging genomic information to predict the functional attributes of individual taxa. The field is now poised to identify how we can manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve our understanding of how terrestrial ecosystems will respond to environmental change.
Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolism and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.
This study was aimed to investigate the direction and magnitude of soil organic carbon (SOC) dynamics and the underlying mechanisms following agricultural abandonment in a subtropical karst area, southwest China. Two post-agriculture succession sequences including grassland (~10 years), shrubland (~29 years), secondary forest (~59 years) and primary forest with cropland as reference were selected. SOC and other soil physicochemical variables in the soil depth of 0–15 cm (representing the average soil depth of the slope in the studied area) were measured. SOC content in the grassland was not significantly elevated relative to the cropland (42.0 ± 7.3 Mg C ha⁻¹). SOC content in the shrubland reached the level of the primary forest. On average, SOC content for the forest was 92.6 ± 4.2 Mg C ha⁻¹, representing an increase of 120.4 ± 10.0% or 50.6 ± 4.2 Mg ha⁻¹ relative to the cropland. Following agricultural abandonment, SOC recovered to the primary forest level in about 40 years with a rate of 1.38 Mg C ha⁻¹ yr⁻¹. Exchangeable Ca and Mg were found to be the strongest predictors of SOC dynamics. Our results suggest that SOC content may recover rapidly following agricultural abandonment in the karst region of southwest China.
Polysaccharide lyases are the products of various microorganisms, bacteriophage and some eukaryotes. All such enzymes cleave a hexose‐1,4‐α‐ or β‐uronic acid sequence by β‐elimination. They are in some examples, the only known type of enzymes degrading their polyanionic substrates. Although only a small number of these enzymes have been exhaustively studied, the pectin lyases of bacterial origin have proved to be of interesting crystal structure containing a parallel β‐helix domain. Alginate and heparin lyases may yield products with biotechnological potential.
The effects of natural succession on plant communities and soil variables have been established, but changes in microbial communities and their response to plants and soils have not been well characterized in secondary succession. We investigated the changes in soil properties and plant and soil microbial communities during the secondary succession on abandoned cropland in the Loess Plateau of China using high-throughput sequencing of the 16S rRNA gene. The study analyzed a chronosequence of farmland undergoing spontaneous succession after being abandoned for 0 (farmland), 5, 10, 15, 20 and 30 years(y). Plant community metrics including percent cover, and above/belowground biomass, first decreased in the initial stage (<10 y) and then increased during the succession. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacteria across all succession. Bacterial communities transitioned from Acidobacteria-dominant to Proteobacteria-dominant communities during the 30 years of succession. Levels of soil organic carbon (C), total nitrogen (N), nitrate N and bacterial diversity were lower soon (<5 years) after abandonment compared to the farmland, but they could recover to farmland levels after 15–20 years and were much improved after continued succession. Plant and bacterial community diversities (Shannon index and species richness) changed along successional time, but they showed different patterns, suggesting an incongruous process between plant and microbial succession. Organic C, total N, available N, and available P contents were significantly correlated with the abundance of most bacterial groups and the Shannon index, indicating the dependence of bacterial community diversity on soil nutrient supply.