Diversity Of Soil Microbial Communities Research Articles

Drought and vegetation restoration lead to shifts in soil microbial diversity and co-occurrence networks in California coastal prairie

Abstract Background and aims Both drought and vegetation restoration can have dramatic effects on plant community composition, but how they influence soil microbial community diversity, structure, and co-occurrence networks remain less well known. Methods To better understand the regulatory mechanisms of drought and vegetation restoration on soil microorganisms, we planted 12 native species in precipitation manipulation experimental plots in an invaded coastal grassland in California, USA. We measured soil bacterial and fungal community composition by amplicon sequencing, and quantified plant species richness and coverage in the third experimental year. Results Our results showed that drought significantly altered soil bacterial diversity and composition; however, neither drought nor vegetation restoration had significant effects on fungal diversity and composition. The control plots had the most cooperative interactions (greatest number of correlations) among bacterial and/or fungal species, while drought plots yielded the most complex co-occurrence network with the highest modularity and clustering coefficient. Structural equation modeling revealed that plant species richness, net gains, and soil moisture played dominant roles in shaping bacterial community structure. Drought and bacterial community structure directly affected fungal community structure. Plant dominant species cover, common species cover, and bacterial diversity were the key drivers in regulating the microbial co-occurrence network complex. Conclusion We conclude that soil bacterial and fungal communities differ in their responses to abiotic and biotic environmental changes, which may weaken the interspecies interactions among soil microorganisms.

Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system

BackgroundThe soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push–pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with those obtained from maize-monoculture (Mono) cropping system.ResultsThe PPT cropping system changed the composition and diversity of soil and maize-root microbial communities, and led to notable improvements in soil physicochemical characteristics compared to that of the Mono cropping system. Distinct bacterial and fungal genera played a crucial role in influencing the variation in microbial diversity within these cropping systems. The relative abundance of fungal genera Trichoderma, Mortierella, and Bionectria and bacterial genera Streptomyces, RB41, and Nitrospira were more enriched in PPT. These microbial communities are associated with essential ecosystem services such as plant protection, decomposition, carbon utilization, bioinsecticides production, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Conversely, pathogenic associated bacterial genus including Bryobacter were more enriched in Mono-root. Additionally, the Mono system exhibited a high relative abundance of fungal genera such as Gibberella, Neocosmospora, and Aspergillus, which are linked to plant diseases and food contamination. Significant differences were observed in the relative abundance of the inferred metabiome functional protein pathways including syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation.ConclusionPush–pull cropping system positively influences soil and maize-root microbiomes and enhances soil physicochemical properties. This highlights its potential for agricultural and environmental sustainability. These findings contribute to our understanding of the diverse ecosystem services offered by this cropping system where it is practiced regarding the system's resilience and functional redundancy. Future research should focus on whether PPT affects the soil and maize-root microbial communities through the release of plant metabolites from the intercrop root exudates or through the alteration of the soil's nutritional status, which affects microbial enzymatic activities.

Soil microbial community are more sensitive to ecological regions than cropping systems in alpine annual grassland of the Qinghai-Tibet Plateau.

Modern agriculture emphasizes the design of cropping systems using ecological function and production services to achieve sustainability. The functional characteristics of plants (grasses vs. legumes) affect changes in soil microbial communities that drive agroecosystem services. Information on the relationship between legume-grass mixtures and soil microorganisms in different ecological zones guides decision-making toward eco-friendly and sustainable forage production. However, it is still poorly understood how cropping patterns affect soil microbial diversity in alpine grasslands and whether this effect varies with altitude. To fill this gap in knowledge, we conducted a field study to investigate the effects of growing oats (Avena sativa L.), forage peas (Pisum sativum L.), common cornflower (Vicia sativa L.), and fava beans (Vicia faba L.) in monocultures and mixtures on the soil microbial communities in three ecological zones of the high alpine zone. We found that the fungal and bacterial community structure differed among the cropping patterns, particularly the community structure of the legume mixed cropping pattern was very different from that of monocropped oats. In all ecological zones, mixed cropping significantly (p < 0.05) increased the α-diversity of the soil bacteria and fungi compared to oat monoculture. The α-diversity of the soil bacteria tended to increase with increasing elevation (MY [2,513 m] < HZ [2,661 m] < GN [3,203 m]), while the opposite was true for fungi (except for the Chao1 index in HZ, which was the lowest). Mixed cropping increased the abundance of soil fungi and bacteria across ecological zones, particularly the relative abundances of Nitrospira, Nitrososphaera, Phytophthora, and Acari. Factors affecting the bacterial community structure included the cropping pattern, the ecological zone, water content, nitrate-nitrogen, nitrate reductase, and soil capacity, whereas factors affecting fungal community structure included the cropping pattern, the ecological zone, water content, pH, microbial biomass nitrogen, and catalase. Our study highlights the variation in soil microbial communities among different in alpine ecological regions and their resilience to cropping systems. Our results also underscore that mixed legume planting is a sustainable and effective forage management practice for the Tibetan Plateau.

Soil, Plant, and Microorganism Interactions Drive Secondary Succession in Alpine Grassland Restoration.

Plant secondary succession has been explored extensively in restoring degraded grasslands in semiarid or dry environments. However, the dynamics of soil microbial communities and their interactions with plant succession following restoration efforts remain understudied, particularly in alpine ecosystems. This study investigates the interplay between soil properties, plant communities, and microbial populations across a chronosequence of grassland restoration on the Qinghai-Tibet Plateau in China. We examined five succession stages representing artificial grasslands of varying recovery durations from 0 to 19. We characterized soil microbial compositions using high-throughput sequencing, enzymatic activity assessments, and biomass analyses. Our findings reveal distinct plant and microbial secondary succession patterns, marked by increased soil organic carbon, total phosphorus, and NH4+-N contents. Soil microbial biomass, enzymatic activities, and microbial community diversity increased as recovery time progressed, attributed to increased plant aboveground biomass, cover, and diversity. The observed patterns in biomass and diversity dynamics of plant, bacterial, and fungal communities suggest parallel plant and fungal succession occurrences. Indicators of bacterial and fungal communities, including biomass, enzymatic activities, and community composition, exhibited sensitivity to variations in plant biomass and diversity. Fungal succession, in particular, exhibited susceptibility to changes in the soil C: N ratio. Our results underscore the significant roles of plant biomass, cover, and diversity in shaping microbial community composition attributed to vegetation-induced alterations in soil nutrients and soil microclimates. This study contributes valuable insights into the intricate relationships driving secondary succession in alpine grassland restoration.

Remediation of cadmium-contaminated soil by biochar-loaded nano-zero-valent iron and its microbial community responses

At present, cadmium (Cd)-contaminated soil has been increasingly serious, which is adverse to soil health. In this study, biochar (BC) and biochar-loaded nanoscale zero-valent iron (nZVI@BC) were synthesized for remediation of Cd-contaminated soil. The effects of various factors including reaction time, dosage, nZVI loading on Cd fractionation, soil available iron, pH, CEC, and soil enzyme activity were comprehensively discussed. It can be concluded that nZVI@BC exhibited more excellent immobilization effect of Cd, and was positively correlated with dosage and reaction time, but negatively related to nZVI loading. As a result, 5% nZVI@BC(1:3) performed the best. Soil available iron, pH, and CEC were significantly enhanced with increasing nZVI loading. The immobilization mechanism was analyzed, including ion exchange, physical adsorption, surface complexation, electrostatic attraction as well as co-precipitation. Besides, nZVI@BC remarkably promoted soil catalase activity, but inhibited urease and FDA hydrolase activities. Furthermore, the effects and differences on the diversity, abundance, and species composition of soil microbial communities were deeply explored. The order of bacterial community richness in each group was CK > Cd > BC > nZVI@BC, and the bacterial community diversity was CK > nZVI@BC > Cd > BC. The greatest difference of species abundance composition was observed between nZVI@BC treatment group and the control. Additionally, forty-three biomarkers were screened, which primarily belonged to Proteobacteria, Gemmatimonadetes, Firmicutes, and Actinobacteria. This study will provide the profound theoretical basis for nZVI@BC remediation of Cd-contaminated soil and its microbial community responses.

Parental material and climate jointly determine the biomass and diversity of soil microbial communities along an elevational gradient on a subtropical karst mountain

AbstractAimClimate is widely understood to determine elevational patterns of soil microbial communities, whereas the effects of parental material are uncertain. Changes in the composition of parental materials along elevational transects could also affect soil microbial communities by influencing soil pH and nutrient availability. Here, we aim to illustrate the combined effects of climate and parental material on the biomass and composition of soil microbial communities along an elevational transect.LocationA subtropical forest on a karst mountain (Mt. Jinfo), China.TaxonBacteria and Fungi.MethodsWe use phospholipid fatty acid analysis (PLFA) and DNA amplicon high‐throughput sequencing to determine biomass and diversity patterns of soil microbial communities along a subtropical elevational gradient with contrasting parental materials (limestone and clasolite).ResultsWe observed that the microbial communities were more diverse (α‐diversity) and productive (biomass) on limestone than on clasolite. Additionally, we found that parental material played a role in shaping the composition (β‐diversity) of soil microbial communities along the elevational gradient. The impact of climate on soil microbial communities was found to be significant, albeit relatively weak. Structural equation models provided evidence for both direct and indirect effects of climate and parental material on microbial biomass and α‐diversity along the elevational gradient. Notably, the changes in soil pH, influenced by both parental material and climate, were identified as a key factor driving these effects.Main ConclusionsOur results underline the importance of both climate and parental material variations in space‐for‐time studies investigating soil microbial communities along elevational gradients.

Selenium Fertilizer Improves Microbial Community Structure and Diversity of Rhizospheric Soil and Selenium Accumulation in Tomato Plants

ABSTRACT Selenium (Se) is an essential microelement in living organisms, and has a beneficial effect on plant growth and stress tolerance at low concentrations. Se biofortification is commonly practiced in agriculture and is considered the best method for increasing human Se uptake. This study aimed to investigate the effects of Se fertilizer application on Se accumulation and microbial communities in the rhizospheric soil of tomato plants. A pot experiment with five treatments, i.e. (a) non-Se fertilizer as control (Ck) and Se fertilizer in the form of (b) sodium selenite (1 mg kg−1), (c) sodium selenite (5 mg kg−1), (d) sodium selenate (1 mg kg−1), and (e) sodium selenate (5 mg kg−1) was set up. The results showed that Se content in the tomato plants’ parts gradually increased with an increasing concentration of sodium selenate or selenite. Sodium selenate significantly increased tomato yield and improved Se accumulation in tomato plants. Se-treated treatments decreased the abundance of soil microbial community, and had no effect on the Chao1 and Shannon indices of them. Furthermore, Se application increased the relative abundance of Acidobacteriota and Actinobacteriota involved in the decomposition of organic matter, reducing Bacteriodota and Ascomyta, and significantly affected the bacterial community structure. Thus, Se fertilizer application increased the crop yield, improved Se accumulation, and the structure and diversity of rhizospheric soil microbial community in the tomato plants. In line with our experiment, 5 mg kg−1 concentration selenate is a reasonable way to harvest Se-enriched tomatoes.

Functional diversity of microbial communities in herbaceous vegetation patches in coal mine heaps

AbstractCoal mine heaps represent unique novel environments, suitable for studying plant succession and its influence on the activity of microbes inhabiting the rhizosphere. Our aim was to verify if the functional diversity and catabolic activity of soil microorganisms would increase along with the plant succession from non‐vegetated and forbs‐dominated to grass‐dominated communities. The study was conducted on coal mine heaps located in Upper Silesia (Southern Poland), focusing on non‐vegetated patches, patches dominated by forbs–Tussilago farfara and Daucus carota (in the early stages of succession), and by grasses–Poa compressa and Calamagrostis epigejos (in later stages of primary succession). The catabolic activity and functional diversity of soil microbial communities were analyzed based on community‐level physiological profiles using BIOLOG EcoPlatesTM and the activity of dehydrogenase, alkaline phosphatase, acid phosphatase, and urease. Our results showed that spontaneous vegetation on coal mine heaps strongly affects the physicochemistry of the substrate and the functional diversity of soil microbial communities. Grasses' rhizosphere was hosting more active and functional diversified microbial communities, while non‐vegetated and T. farfara‐vegetated patches were accompanied by a reduced development of soil microbiota. Furthermore, grasses were mainly associated with a substantial delivery of plant litter to the substrate, providing a source of carbon for microorganisms.

Fertilization enhances rice productivity by promoting phosphorus uptake and altering soil microbiota

Fertilization can enhance crop yield and improve soil health. However, its effects on nutrient uptake, soil microbiota, and rice yield remain unclear. Herein, we designed a double-cropping system with different fertilization treatments to determine their contributions to paddy soil agroecosystem and rice yield. Soil samples were collected before planting the early rice, after harvesting early rice, and after harvesting the late rice. Soil physicochemical properties, and rice yield, and rice nutrient (total nitrogen, phosphorus, and potassium contents) were determined. Variation of soil microbiota were also determined by high-throughput sequencing. We found that soil potassium content significantly improved during the planting process (P < 0.05), while rice phosphorus displayed significant variation under fertilization (P < 0.05). Notably, late rice yield was significantly higher than early rice yield (P < 0.001) after fertilization treatment. Furthermore, rice yield was positively correlated with available soil phosphorus (P < 0.05), indicating that fertilization promoted phosphorus uptake. Organic fertilizer altered the soil microbiota and increased Chloroflexi phyla abundance, while organic fertilizer combined with a compound microbial agent increased the diversity of soil microbial communities. A partial least squares path model revealed that fertilizer treatment directly positively affected rice yield by influencing phosphorus uptake and Shannon index (P < 0.01). Collectively, this study demonstrates that organic fertilization with compound microbial agents can stabilize soil nutrients, increase soil microbial diversity, and improve rice yield, thereby offering a guide for enhancing fertilizer utilization and improving agroecosystems.

Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China

Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the “space instead of time” approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.

Response of rhizosphere soil physicochemical properties and microbial community structure to continuous cultivation of tobacco

PurposeThe health of rhizosphere soil microorganisms is an important indicator to evaluate soil quality. Therefore, understanding the response of rhizosphere soil microorganisms to tobacco crop succession is crucial for promoting the sustainable development of agriculture.MethodsThe microbial diversity and community structure of rhizosphere soil in continuous cropping and non-cropped tobacco for 7 years were analyzed by the Illumina platform.Result(1) Continuous cropping tobacco cause rhizosphere soil acidification and reduction in alkaline nitrogen (AN) and soil organic matter (SOM). (2) Continuous cropping tobacco reduces the diversity of rhizosphere soil microbial communities, increasing harmful functional microorganisms and declining beneficial ones. (3) The abundance of bacteria that perform nitrification and saprophytic fungi in the rhizosphere soil of continuous cropping areas decreases, inhibiting carbon and nitrogen cycling processes. (4) The composition and diversity of the soil rhizosphere microbial community are affected by the imbalance in the physicochemical property of the rhizosphere.ConclusionContinuous cropping tobacco cause rhizosphere soil acidification and nutrient imbalance, and the carbon and nitrogen cycles involved in microorganisms were damaged. Furthermore, the decreased diversity of rhizosphere soil microorganisms and the increased abundance of pathogenic fungi contribute to the continuous cropping obstacles of tobacco.

Mitigation of aeolian erosion of loess soil by Bio-Stimulated microbial induced calcite precipitation

Microbial-induced calcite precipitation (MICP) is a soil amelioration technique that addresses various environmental and engineering concerns. Here, we present a study focusing on aeolian erosion control of loess soil from the Negev Desert (Israel). Changes in the treated soil's chemical, physical, and microbial community (abundance and diversity) were characterized following bio-stimulation of native, urea-hydrolyzing soil bacteria to achieve MICP. Bio-stimulation of the loess soil was induced in liquid media (batch experiments) and by spraying soil trays with stimulation media (urea and yeast extract). These experiments showed that the Negev loess could be readily stimulated to induce bacterial urea hydrolysis. Three to four daily sprayings were sufficient to achieve effective bio-stimulation, evidenced by a high hydrolysis rate and an alkaline pH. Erodibility experiments on a decimeter scale (50 cm x 50 cm trays) were performed on loess sprayed with treatment media with varying concentrations of urea and CaCl2, with a constant 1:1 M ratio. The effectiveness of the treatments was studied in a wind tunnel and by image analysis of desiccation cracks. Upscaling of the experiments to the large trays revealed a more complicated reality with urease activity, community composition, and calcium carbonate precipitation depending on the concentration of the treatment medium. Specifically, we show that a twofold reduction in the area and length of the desiccation cracks can be achieved by spraying the soil with a 0.5 M solution, resulting in effective MICP or a high concentration treatment (>1M solution) without achieving MICP. Our results show that erosion mitigation in loess soil depends on an interplay between biotic and abiotic processes based on the treatment media concentration and provides a necessary step for upscaling the bio-stimulated MICP strategy for future field implementations.

Interaction effects of pH and land cover on soil microbial diversity are climate-dependent.

Factors regulating the diversity and composition of soil microbial communities include soil properties, land cover and climate. How these factors interact at large scale remains poorly investigated. Here, we used an extensive dataset including 715 locations from 24 European countries to investigate the interactive effects of climatic region, land cover and pH on soil bacteria and fungi. We found that differences in microbial diversity and community composition between land cover types depended on the climatic region. In Atlantic, Boreal and Continental regions, microbial richness was higher in croplands and grasslands than woodlands while richness in Mediterranean areas did not vary significantly among land cover types. These differences were further related to soil pH, as a driver of bacterial and fungal richness in most climatic regions, but the interaction of pH with land cover depended on the region. Microbial community composition differed the most between croplands and woodlands in all regions, mainly due to differences in pH. In the Mediterranean region, bacterial communities in woodlands and grasslands were the most similar, whereas in other regions, grassland and cropland-associated bacteria showed more similarity. Overall, we showed that key factors interact in shaping soil microbial communities in a climate-dependent way at large scale.

Effects of coffee pericarp and litter mulsching on soil microbiomes diversity and functions in a tropical coffee plantation, South China.

In recent decades, ecological cyclic cultivation models have attracted increasing attention, primarily because the decomposition of crop residues and litter enhances soil organic matter content, thereby altering the soil microenvironment and regulating the diversity and functions of soil microbial communities. However, the effects of different coffee waste mulching on the diversity of soil microbial communities and their functions are still unclear. Therefore, this study set up four kinds of covering treatments: uncovered coffee waste (C), covered coffee litter (L), covered coffee pericarp (P), and both covered coffee litter and pericarp (PL). The results showed that compared to the control, coffee pericarp mulching significantly increased the soil available potassium (SAK) content by 18.45% and alkali hydrolyzed N (SAN) content by 17.29%. Furthermore, coffee pericarp mulching significantly increased bacterial richness and diversity by 7.75 and 2.79%, respectively, while litter mulching had little effect on bacterial abundance and diversity was smaller. The pericarp mulching significantly increased the abundance of Proteus by 22.35% and the abundance of Chlamydomonas by 80.04%, but significantly decreased the abundance of Cyanobacteria by 68.38%, while the coffee litter mulching significantly increased the abundance of Chlamydomonas by 48.28%, but significantly decreased the abundance of Cyanobacteria by 73.98%. The increase in soil SAK promoted bacterial Anoxygenic_photoautotrophy, Nitrogen_respiration, Nitrate_respiration, Nitrite_respiration, and Denitrification functions. The above results indicate that the increase in available soil potassium and alkali hydrolyzed N content under coffee pericarp cover is the main reason for promoting the diversity and richness of bacterial community and promoting the changes in bacterial community structure and function. The use of coffee pericarps in coffee plantations for ecological recycling helps to improve the diversity of the soil microbial community and maintain the relative stability of the microbial community structure and function, promoting soil health conservation and the sustainable development of related industries.

Alfalfa cropping is superior to cotton and rapeseed cropping in improving the quality and microbial diversity of reclaimed saline soils

ABSTRACT Soil salinisation has led to increasing abandonment of farmlands in the arid region of northwest China, and the cultivation of cash crops has become an important way to reuse abandoned farmlands and remediate saline soils. In this study, the effects of cotton (Cot), alfalfa (Alf), and rapeseed (Rap) cropping on the bacterial and fungal communities in saline soil were compared based on high-throughput sequencing. The results showed that soil pH and electrical conductivity (EC) of the Cot, Alf, and Rap groups decreased significantly compared with those of bare land (CK). Especially, soil pH (8.3) and EC (0.93 mS cm-1) of the Alf group decreased the most, and the contents of total nitrogen (TN) and total phosphorus (TP) increased the most, which increased by 250% and 91.4%, respectively compared with those of the CK (p < 0.05). Actinobacteriota and Proteobacteria were the dominant bacterial phyla in the three groups, Ascomycota and Basidiomycota were the dominant fungal phyla. The diversity of soil bacterial and fungal communities in the Alf group was higher than that in the Cot and Rap groups. The results of RDA and PERMANOVA analysis showed that soil pH, EC, C/N ratio, and TN were the main factors affecting soil bacterial and fungal communities in the three groups. In general, Cot, Alf, and Rap cropping all could reduce soil pH and EC and improve soil microbial community structure and diversity, but Alf cropping had the best effects in improving saline soil quality and bacterial and fungal diversity.

Seasonal Changes in the Soil Microbial Community Structure in Urban Forests.

Urban forests play a crucial role in the overall health and stability of urban ecosystems. Soil microorganisms are vital to the functioning of urban forest ecosystems as they facilitate material cycling and contribute to environmental stability. This study utilized high-throughput sequencing technology to examine the structural characteristics of bacterial and fungal communities in the bulk soil of six different forest stands: Phyllostachys pubescens (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Soil samples were collected from each forest stand, including the corners, center, and edges of each plot, and a combined sample was created from the first five samples. The results revealed that among the bacterial communities, ZKG exhibited the highest alpha diversity in spring, while ZL demonstrated the highest alpha diversity in both summer and autumn. Proteobacteria was the most abundant bacterial phylum in all six forest stand soils. The dominant fungal phylum across the six forest stands was identified as Ascomycota. Notably, the microbial community diversity of SBL bulk soil exhibited significant seasonal changes. Although ZL exhibited lower bacterial community diversity in spring, its fungal community diversity was the highest. The bulk soil microbial diversity of ZL and SSL surpassed that of the other forest stands, suggesting their importance in maintaining the stability of the urban forest ecosystem in the Zhuyu Bay Scenic Area. Furthermore, the diversity of the bulk soil microbial communities was higher in all six stands during spring compared to summer and autumn. Overall, this study provides valuable insights into the seasonal variations of bulk soil microbial communities in urban forests and identifies dominant tree species, offering guidance for tree species' selection and preservation in urban forest management.

Overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community.

A "grazing ban" policy has been implemented in some pastoral areas in China to fence degraded grasslands for restoration. However, fencing increased grazing pressures in unmanaged grasslands. Based on the mechanism of negative edge effect, we investigated whether overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community using a sample in Hulun Buir of Inner Mongolia, in order to optimize the "grazing ban" policy. Plant and soil were sampled in areas 30 m away from the fence in unmanaged grassland (UM) and in areas 30 m (adjacent to UM) and 30-60 m (not adjacent to UM) away from the fence in the grazing-banned grassland (F-30 m and F-60 m). The species richness and diversity of plant communities and the ASV number of fungal communities significantly decreased in F-30 m and UM, and the Simpson index of the bacterial community significantly decreased in F-30 m compared with F-60 m. The abundance of fungi involved in soil organic matter decomposition significantly decreased and the abundance of stress-resistant bacteria significantly increased, while the abundance of bacteria involved in litter decomposition significantly decreased in UM and F-30 m compared with F-60 m. The simplification of plant communities decreased in soil water and total organic carbon contents can explain the variations of soil microbial communities in both UM and F-30 m compared with F-60 m. The results of PLS-PM show that changes in plant community and soil microbial function guilds in UM may affect those in F-30 m by changing soil water and total organic carbon contents. These results indicate that overgrazing on unmanaged grassland interfered with the restoration of adjacent grazing-banned grassland by affecting soil properties and microbial community. The grazing-banned grasslands should be adjusted periodically in order to avoid negative edge effects.

Effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, China.

Soil microorganisms can be used as one of the important indicators of wetland ecosystem restoration. To study the effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, we employed a "time and space parallel" method. Four restoration stages, namely corn field (Corn), short-term restoration wetland (2 years, ST), long-term restoration wetland (8 years, LT) and natural wetland (>25 years, NW), were selected to represent the restoration time and geographical location in Naolihe Nature Wetland. We investigated the composition and diversity of soil microbial communities in different restoration wetland (from corn fields to natural wetlands) by using 16S rRNA and ITS rRNA gene sequencing. We also performed chemical experiments to measure soil enzyme activity and physicochemical properties at each sampling site. The results showed that soil physicochemical properties and enzyme activities significantly differed with the extension of wetland restoration years (p < 0.05). Proteobacteria, Acidobacteria, and Actinobacteria are the most dominant phyla in bacterial. The alpha diversity of soil bacteria was the highest in the corn field (Corn), and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. There are two most dominant phyla (Ascomycota and Mucoromycota) in fungal. However, the alpha diversity of soil fungi was the lowest in the Corn and LT stage, and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. The research findings indicated that the changes in soil physicochemical properties with the extension of wetland restoration years play a significant role in shaping the structure and diversity changes of soil microbial communities. Through the analyses of bacterial and fungal functions using the FUNGuild and FAPROTAX databases, the results showed that the abundance of aerobic bacteria in the soil increased more than that of anaerobic bacteria as the wetland restoration years prolonged, while the abundance of saprotrophic, symbiotic, and pathogenic fungi in the soil significantly decreased with the prolonged wetland restoration years. This study will help us better understand the process of restoration after farmland abandonment, providing valuable reference information for the implementation of a series of wetland ecological restoration projects in the future.

Impact of climate warming on soil microbial communities during the restoration of the inner Mongolian desert steppe.

Grazer exclosure is widely regarded as an effective measure for restoring degraded grasslands, having positive effects on soil microbial diversity. The Intergovernmental Panel on Climate Change (IPCC) predicts that global surface temperatures will increase by 1.5-4.5°C by the end of the 21st century, which may affect restoration practices for degraded grasslands. This inevitability highlights the urgent need to study the effect of temperature on grassland soil microbial communities, given their critical ecological functions. Here, we assessed the effects of heavy grazing (control), grazer exclosure, and grazer exclosure plus warming by 1.5°C on soil microbial community diversity and network properties as well as their relationships to soil physicochemical properties. Our results showed that grazer closure increased soil microbial richness relative to heavy grazing controls. Specifically, bacterial richness increased by 7.9%, fungal richness increased by 20.2%, and the number of fungal network nodes and edges increased without altering network complexity and stability. By contrast, grazer exclosure plus warming decreased bacterial richness by 9.2% and network complexity by 12.4% compared to heavy grazing controls, while increasing fungal network complexity by 25.8%. Grazer exclosure without warming increased soil ammonium nitrogen content, while warming increased soil nitrate nitrogen content. Soil pH and organic carbon were not affected by either exclosure strategy, but nitrate nitrogen was the dominant soil factor explaining changes in bacterial communities. Our findings show that grazer exclosure increases soil microbial diversity which are effective soil restoration measures for degraded desert steppe, but this effect is weakened under warming conditions. Thus, global climate change should be considered when formulating restoration measures for degraded grasslands.

Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.

Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.