Role Of Soil Microbes Research Articles

Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

AbstractMicrobes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession.

Role of soil microbes in enhancing crop heterosis

Role of soil microbes in enhancing crop heterosis

Impacts of Climate change on soil microbial diversity, distribution and abundance

Climate change, driven by anthropogenic activities, has far-reaching consequences for our planet. Among its many impacts, changes in temperature, elevated carbon dioxide levels, and shifts in greenhouse gas concentrations significantly affect soil ecosystems. In particular, soil microbial communities play a pivotal role in nutrient cycling, organic matter decomposition, and overall soil health. Soil microbial communities respond differently to the effects of climate change, like elevated warming and precipitation. The change in climatic conditions is reported to be adversely affecting soil biological activity directly through either drying or wetting of soil or affecting their associated plants. This review delves into the intricate relationship between climate change and soil microbial abundance, diversity, and distribution. The paper also discusses climatic change pressure on soil enzymatic activity and microbial biomasses, as well as soil faunal activity, as they are key indicators of soil health in a changing climate. Soil microbial communities cope with climate change by changing their diversity and physiological characteristics and by changing their symbiotic plants, which indicates the role of soil microbes in withstanding the negative impact of climate change.

Restoration of open ecosystems in the face of climate change

Open ecosystems occur all around the world in various forms including temperate and tropical grasslands, savannas, shrublands, heathlands, among others. They are home to unique biodiversity, provide key ecosystem services and sustain traditional livelihoods of nearly two billion people. In the face of ongoing climate change, practitioners aiming to restore open ecosystems need the support of the scientific community more than ever. The aim of this Special Issue (SI) is to provide an attention-grabbing collection of high-quality publications addressing the growing challenges of open ecosystems restoration. The SI contains 14 papers that fill various, often interdisciplinary knowledge gaps. Three papers deal with the challenges of identifying the right target states, including the genetic composition of constituting plant species, for restoration under changing environmental conditions and competing stakeholder interests. Five papers advance our understanding on the appropriate timing and methodological toolkit to actively ignite re-assembly of the target plant communities, while two papers focus on situations where spontaneous processes can still also be relied on. The interaction of open ecosystems health and recovery with higher trophic levels, particularly grazers, is also discussed in three papers. Finally, a review paper systematically identifies further knowledge gaps, such as the role of soil microbes in grassland recovery and makes clear guidelines how to fill them. Due to the variety of topics and the rigorous content, this SI provides strong support for open ecosystems restoration policy and practice under the UN Decade on Ecosystem Restoration and beyond.

The contribution of microbial necromass to soil organic carbon and influencing factors along a variation of habitats in alpine ecosystems

A growing consensus is reached that microbes contributes to regulating the formation and accumulation of soil organic carbon (SOC). Nevertheless, less is known about the role of soil microbes (necromass, biomass) in SOC accumulation in different habitat conditions in alpine ecosystems. To address this knowledge gap, the composition and distribution of amino sugars (ASs) and phospholipid fatty acids (PLFAs) as biomarkers of microbial necromass and biomass were investigated in forest, meadow and wetland soil profile (0–40 cm) of Mount Segrila, Tibet, China, as well the contribution of bacterial and fungal necromass to SOC. The results revealed that microbial necromass carbon contributed 45.15 %, 72.51 % and 78.08 % on average to SOC in 0–40 cm forest, meadow and wetland soils, respectively, and decreased with microbial biomass. Fungal necromass contributed more to SOC in these habitats than bacterial necromass. Microbial necromass increased with microbial biomass and both of them decreased with soil depth in all habitats. The necromass accumulation coefficient was significantly correlated with microbial necromass and biomass, affected by habitat and soil moisture. Structural equation model indicated that soil abiotic factors indirectly mediated the accumulation of SOC through microbial necromass and biomass. This study revealed that different habitats and soil depths control considerably soil physicochemical properties and microbial community, finally influencing SOC accumulation in alpine ecosystems, which emphasized the influence of abiotic factors on microbial necromass and biomass for SOC accumulation in alpine ecosystems.

Distribution of Genes and Microbial Taxa Related to Soil Phosphorus Cycling across Soil Depths in Subtropical Forests

Although many studies have focused on the roles of soil microbes in phosphorus (P) cycling, little is known about the distribution of microbial P cycling genes across soil depths. In this study, metagenomic sequencing was adopted to examine the differences in the abundance of genes and microbial taxa associated with soil P cycling between organic and mineral soil in subtropical forests. The total relative abundance of inorganic P solubilizing genes was the highest, that of P starvation response regulating genes was second, and organic P mineralizing genes was the lowest. The soil organic carbon concentration, N:P ratio, and available P concentration were higher in the organic soil than the mineral soil, resulting in abundances of organic P mineralizing genes (appA and 3-phytase), and inorganic P cycling genes (ppa), whereas those of the inorganic P cycling genes (gcd and pqqC) and the P starvation response regulating gene (phoR) were higher in mineral soil. The four bacteria phyla that related to P cycling, Proteobacteria, Actinobacteria, Bacteroidetes, and Candidatus_Eremiobacteraeota were higher in organic soil; conversely, the three bacteria phyla (Acidobacteria, Verrucomicrobia, and Chloroflexi) and archaea taxa were more abundant in mineral soil. Therefore, we concluded that the distribution of genes and microbial taxa involved in soil P cycling differed among soil depths, providing a depth-resolved scale insight into the underlying mechanisms of P cycling by soil microorganisms in subtropical forests.

IMPACT OF CLIMATE CHANGE ON SOIL HEALTH: EMERGING ISSUES

Climate change is the single biggest threat facing humanity. Soil health is impacted by climate change. Climate change effects soil formation, soil structure and soil health which are complex processes affecting each other. Impact assessment of climate change on agriculture, horticulture and forests did not consider for a long time the soil quality issues. In this review, impacts of climate change on soil texture, soil structure, porosity, soil physico- chemical-biological components are reviewed. Role of soil microbes, soil carbon and crop diversication on soil health are also discussed.

Role of Sedum alfredii and soil microbes in the remediation of ultra-high content heavy metals contaminated soil

Ultra-high content of heavy metals (UHHMs) poses a threat to soil health and agricultural products safety, in turn causing harm to human health through the food chain. Phytoremediation has proven to be an effective technique for restoration of soil contaminated with a single or several conventional content of heavy metals, whereas the effectiveness of phytoremediation for UHHMs-contaminated soil is unclear. In this study, we investigated the effectiveness of phytoremediation for UHHMs-contaminated soil and the role of soil microbes in the process of phytoremediation. Results showed that the Sedum alfredii grew well in UHHMs-contaminated soil, although the shoot height, biomass, and accumulation of heavy metals were slightly reduced due to the stress of UHHMs. Soil microbiome analysis demonstrated that both the number and diversity of microbes decreased in UHHMs-contaminated soil. However, the dominant species Patescibacteria proliferated to varying degrees under the exposure of various UHHMs. Patescibacteria is closely related to the functional genes regarding transport of various heavy metals. Given that Patescibacteria exhibits a strong migration ability in soil, it is likely involved in the transport of various heavy metals from the bulk soil to the rhizosphere. This enhanced the availability of heavy metals in the rhizosphere, which in turn improved the phytoremediation efficiency of the Sedum alfredii. This was further confirmed by structural equation modeling analysis and microbial phenotypes prediction. Findings suggest that using Sedum alfredii to remedy UHHMs-contaminated soil is feasible owing to the facilitation by soil microbes.

Role of Soil Microbes in Disease Control and as a Probiotics

Role of Soil Microbes in Disease Control and as a Probiotics

Soil Microbes as Bioherbicides: An Eco-friendly Approach to Control Striga

Striga, also called witch weed, is a notorious obligate root hemiparasitic weed of global food security crops such as sorghum, maize, millet and upland rice causing considerable yield loss in Sub Saharan Africa. Several Striga control measures have been developed which include cultural, chemical and resistance breeding. However, many of these methods are either not practically successful or are not economically feasible for low-income farmers. Furthermore, the negative effects of agrichemicals on the environment have attracted scientist to look for an alternative weed management strategy. The use of microorganisms naturally occurring in the soil as biological control agents offer an alternative approach to control the parasitic weeds. Soil is the natural home of numerous forms of beneficial microorganism playing vital role in maintaining the dynamic equilibrium. In recent time, soil born microbes, primarily bacteria and fungi, become the most effective Striga management strategy that targets Striga seed bank in the soil. Hence, this review presents a comprehensive and new approach on the roles of soil microbes in fight against Striga.

Role of soil microbes in sustainable crop production and soil health: A review

Abstract. Global food production needs to be increased in order to feed the world’s growing population and at the same time, the reliance on inorganic fertilizers and pesticides should be minimized. To accomplish this goal, the various beneficial associations between plants and soil microorganisms should be explored. The soil microbes are bacteria, actinomycetes, viruses, fungi, nematode, and protozoa. They have an important soil function that has fulfilled several useful tasks in the soil system. Microbes support biological nitrogen fixation of different biological transformations that support the accumulation and utilization of key nutrients, support root and shoot growth processes, disease control, and improve soil quality in crop cultivation. Soil microbes offer nutrient-dense nourishment improved crop production and recycle soil solutions. They play an essential role in decomposing organic matter, cycling nutrients, and fertilizing the soil. Besides, they improve plant growth on various physiological parameters of plants by a number of mechanisms. The mechanism involved in growth promotion includes plant growth regulators, production of different metabolites, and conversion of atmospheric nitrogen into ammonia in direct and indirect ways. In addition, soil microbes offer resistance against diseases. This review outlines the significant impact of soil microbes on sustainable agricultural growth, the benefits of microbes in maintaining soil health, and their interactions.

Bio-fertilizer and rotten straw amendments alter the rhizosphere bacterial community and increase oat productivity in a saline\u2013alkaline environment

Saline–alkaline conditions can limit crop productivity and the role of soil microbes in nutrient cycling in arid and semi-arid regions throughout the world. A better understanding of how soil amendments and plant varieties affect rhizosphere microbial communities in saline–alkaline environments is important for the development of sustainable and productive agricultural systems under these challenging conditions. The objective of this study was to determine the effect of organic soil amendments on crop yield, soil physicochemical properties and rhizosphere bacterial communities of two oat cultivars in a saline–alkaline soil. The experiment was conducted in a semi-arid region of Northern China and involved growing two oat cultivars with varying levels of saline–alkaline tolerance under four different amendment treatments: (1) control (no amendments), (2) bio-fertilizer, (3) rotten straw, and (4) combination of bio-fertilizer and rotten straw. The combined bio-fertilizer and rotten straw amendment treatment resulted in the highest oat yields, reduced soil pH, and increased soil salt content for both cultivars. Baiyan2 (tolerant cultivar) had a higher bacterial α-diversity, relative abundance of Proteobacteria and Acidobacteria, and lower relative abundance of Firmicutes compared to Caoyou1 (sensitive cultivar). The rotten straw treatment and combined amendment treatment decreased bacterial α-diversity and the abundance of Proteobacteria, and increased the abundance of Firmicutes, which were positively correlated with soil salt, available nitrogen, phosphorous and potassium for both cultivars. Our study suggested using tolerant oat cultivars with the combined application of rotten straw and bio-fertilizer could be an effective strategy in remediating saline–alkaline soils.

Influence of soil microbiota on Taxodium distichum seedling performance during extreme flooding events

Plant associations with soil microbiota can modulate tree seedling growth and survival via mutualistic or antagonistic interactions. It is uncertain, however, whether soil microbiota influence seedling growth of coastal trees when exposed to extreme flooding regimes. We evaluated the role of soil microbes in promoting baldcypress (Taxodium distichum) seedling performance under different inundation scenarios and determined the influence of flooding on the colonization of in planta beneficial microbes. Seedlings reared in sterile and non-sterile soil were exposed to three different flooding regimes historically experienced in Louisiana swamps. Seedling growth was assessed, and the colonization by beneficial symbionts such as arbuscular mycorrizhal fungi (AMF), and dark septate endophytes (DSE) was evaluated in harvested roots. Seedlings grown in sterile soil had six times higher growth than seedlings reared in non-sterile soil. As a result, we evaluated pathogen load in the roots by assessing oomycete colonization. Flooding influenced the in planta colonization of DSE and oomycetes, but did not affect the colonization of mutualist AMF fungi. DSE and oomycetes were rarer in flooded conditions, while AMF remained abundant. Seedling biomass production was not correlated with in planta fungal colonization or pathogen load. Soil microbiota can negatively influence baldcypress seedling growth, and no growth benefit was evidenced from the root colonization of mutualist fungi. Flooding can modify baldcypress-fungal interactions by diminishing colonization of DSE. Overall, baldycpress seedlings were more sensitive to the presence of microbiota than flooding, and thus restoration efforts should focus on having a better understanding of plant–microbe interactions in swamps.

Carbon addition reduces labile soil phosphorus by increasing microbial biomass phosphorus in intensive agricultural systems

AbstractAccumulation of inorganic and labile organic phosphorus (P) in intensive agricultural systems leads to P loss from soil which can cause serious environmental problems. Soil microbes are important in mobilizing soil non‐available P, however, little is known about the role of soil microbes in immobilizing P to reduce P loss. Here, we test whether stimulating microbial biomass to immobilize P could reduce the amount of labile P available for leaching. The distribution characteristics of Olsen P, organic P and microbial biomass P were determined in three intensive agricultural systems. In addition, we conducted a pot experiment with three P and four carbon (C) levels. CaCl2 extractable P was measured and used to indicate the risk of P leaching. We found that there was a positive relationship between soil organic C and microbial biomass P. Carbon addition drove the process of P immobilization and reduced CaCl2 extractable P. Microbial biomass P increased by 64% (p < .05) with the addition of C, and Olsen P and CaCl2 extractable P decreased by 28% and 17%, respectively. Our results show that C addition increased microbial immobilization of P and reduced forms of labile P susceptible to leaching. Stimulating microbes to immobilize P by adding C to soils may have the potential to reduce P loss from intensive agricultural systems, reducing their environmental impact.

Effects of soil nutrient availability and ozone on container-grown Japanese larch seedlings and role of soil microbes

The interactive effects of ozone, soil nutrient availability and root microorganisms on physiological, growth, and productivity traits were studied for the first time for Japanese larch (Larix kaempferi) seedlings grown in containers over a growing season, using a free air ozone-concentration enrichment exposure system. High nutrient availability altered leaf and root nutrient dynamics and enhanced plant growth; however, it also enhanced seedling susceptibility to damping-off disease compared to low nutrient availability. Negative effects of elevated ozone, as compared with ambient ozone, on leaf gas exchange and plant stem form were neither offset nor exacerbated by soil nutrient availability and root colonizers. Such negative effects suggest that elevated ozone may have implications for ecological health even when plant vigor is limited by factors other than ozone. Inoculation of roots with ectomycorrhizae had negligible influence on the effects of either soil nutrient availability or ozone. However, this lack of effect may be upon impeded formation of complete mycorrhizal root tips due to factors other than the manipulated variables. B and Na appeared to have an important role in stress responses, so further studies to examine their link with physiological mechanisms as a function of time. This study provides an important perspective for designing forestry practices to enhance seedling health.

Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes.

Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition – specifically, the concentration of the ‘impact aroma compound’ rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined ‘zones’ of inherently ‘low’ or ‘high’ concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.

English

English

Does over-abundance of <i>Bambusa</i> <i>bambos</i> (L.) Voss. alter edaphic properties?

A preliminary study was conducted to determine any modifications to basic soil properties following over-abundance of Bambusa bambos, a native bamboo species, that rapidly expanding its population in Intermediate and Dry Zone forests in Sri Lanka. Soil samples taken from representative sites of bamboo-dominated (BAM) and non-bamboo (NBM) forest patches were analyzed for pH, total nitrogen (N), phosphorus (P), soil moisture and microbial biomass carbon (MBC). A growth assay was carried out with Ricinus communis seedlings in BAM and NBM soils (sterilized/unsterilized) in a glasshouse. The soil analysis revealed significantly higher N, P and moisture in BAM soils than in NBM. BAM soils were clayey in nature compared to silty soils in NBM. Ricinus communis grown in BAM soils performed better throughout the experimental period, perhaps due to higher soil nutrients. Ricinus communis grow better in unsterilized soils irrespective of bamboo, indicating a facilitative role of soil microbes on the growth of plants. The preliminary results suggest that either B. bambos spread has the potential to increase the soil fertility status or else B. bambos expands its population preferably on nutrient-rich clayey soils. Therefore, further studies are needed in order to confirm the impacts of B. bambos on edaphic properties which may eventually influence the growth of co-occurring native species.

Seasonal changes of soil microbial C, N, P and associated nutrient dynamics in a semiarid grassland of north China

Semiarid grasslands are widely distributed in northern China and characterized by marked seasonality. While the role of soil microbes in nutrient cycling is known to be crucial, the nutrient dynamics in relation to changes and turnover of microbial pools over the growth season in semiarid grasslands, are not well understood. In this study, three grasslands with long-term traditional managements (enclosure from sheep grazing for 31 or 18 years, or continuous free overgrazing) were selected to investigate the seasonal fluctuations of microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP). In addition we calculated the turnover rates and fluxes of soil microbial biomass based on their seasonal fluctuations. Plant biomass and N, P uptakes were also assessed to reveal a potential relationship between plant and microbial nutrient pools. We found in this semiarid ecosystem approximately two times lower C:P and N:P ratios in microbial biomass (25:1 and 3:1, respectively) compared with global analysis (46:1 and 6:1, respectively). Enclosure from grazing increased MBC and MBN, while the change patterns of microbial pools were affected by season but not pasture management. Consequently, the turnover rates of microbial biomass as calculated from the seasonal fluctuations were similar in all treatments (around 1.5 year−1 for MBC and MBN, 3 year−1 for MBP). Lower mean stock in soil K2SO4-extractable N but similar in MBN compared with total plant N uptake were observed in all treatments, suggesting N deficiency in this region and the vital role soil microbes play as a stable nutrient pool for plant uptake. In contrast, both NaHCO3-extractable P and MBP stocks were much higher than total plant P uptake, suggesting no P deficiency under current N status.

Soil microorganisms alleviate the allelopathic effect of Eucalyptus grandis × E. urophylla leachates on Brassica chinensis

Soil microbes may be critical players in determining the allelopathic potential of some plants. Low levels of plant community biodiversity in Eucalyptus plantations have been attributed to the allelopathic potential of these tree species. The role of soil microbes in the allelopathic effect of leaf leachates of the hybrid tree Eucalyptus grandis × E. urophylla, was tested in Petri dish assays with Brassica chinensis as a receiver plant. Soils were collected from either a local garden (soil A) or a Eucalyptus plantation (soil B) and half of each soil was sterilized to remove microbes. These soils were then treated with E. grandis × E. urophylla leachates for 0–72 h. Seed germination of B. chinensis was significantly inhibited in soils treated with leaf leachates relative to untreated soils. The inhibitory effect of the leaf leachates was more pronounced in sterilized soils. Total phenolic content was obvious lower in nonsterile leachate-treated soils than in sterile soils. Biomass of B. chinensis was negatively correlated with the total phenolic content in soils. Our findings suggest that soil microbes can alleviate the allelopathic potential of Eucalyptus and thereby its negative impact on plant growth.