Soil Microbial Network Complexity Varies With pH as a Continuum, Not a Threshold, Across the North China Plain

Road Disturbance Shifts Root Fungal Symbiont Types and Reduces the Connectivity of Plant-Fungal Co-Occurrence Networks in Mountains

Roads are currently one of the most disruptive anthropogenic disturbances to mountain ecosystems worldwide. These disturbances can have a profound effect on roadside soil properties and vegetation, typically favouring fast-growing and ruderal species. However, their effect on plant-associated fungal communities and plant-fungal interactions remains largely unknown. In this study, we examined the changes in root-associated fungal communities as well as plant-fungal and fungal-fungal co-occurrence networks along mountain roads from four biogeographical regions. We found that roadsides consistently altered plant and fungal community composition, generally favouring arbuscular mycorrhizal fungi and putative plant pathogens at the expense of ectomycorrhizal fungi. Moreover, roadsides consistently reduced the complexity of plant-fungal and fungal-fungal co-occurrence networks (with 66%-95% and 40%-94% reduction in total edge density, respectively), even though the richness of fungal communities was not reduced and many of the naturally occurring highly connected taxa were still present. Our findings suggest that altered and transient conditions in the roadsides may favour more generalist symbionts like AMF and pathogens with low fidelity for particular hosts as opposed to surrounding natural vegetation which is dominated by symbionts with higher specificity for the host (like ectomycorrhizal fungi). We conclude that road disturbance may have a consistent negative imprint on connectivity between plants and fungi; a consequence that deserves attention as it could render mountain roadside systems unstable and vulnerable to further pressures such as climate change and invasive species.

Microbial diversity in the arid and semi-arid soils of Botswana

To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.

Eucalyptus and Native Broadleaf Mixed Cultures Boost Soil Multifunctionality by Regulating Soil Fertility and Fungal Community Dynamics

The growing recognition of mixed Eucalyptus and native broadleaf plantations as a means of offsetting the detrimental impacts of pure Eucalyptus plantations on soil fertility and the wider ecological environment is accompanied by a clear and undeniable positive impact on forest ecosystem functions. Nevertheless, the question of how mixed Eucalyptus and native broadleaf plantations enhance soil multifunctionality (SMF) and the mechanisms driving soil fungal communities remains unanswered. In this study, three types of mixed Eucalyptus and native broadleaf plantations were selected and compared with neighboring evergreen broadleaf forests and pure Eucalyptus plantations. SMF was quantified using 20 parameters related to soil nutrient cycling. Partial least squares path modeling (PLS-PM) was employed to identify the key drivers regulating SMF. The findings of this study indicate that mixed Eucalyptus and native broadleaf plantations significantly enhance SMF. Mixed Eucalyptus and native broadleaf plantations led to improvements in soil properties (7.60-52.22%), enzyme activities (10.13-275.51%), and fungal community diversity (1.54-29.5%) to varying degrees compared with pure Eucalyptus plantations. Additionally, the mixed plantations exhibit enhanced connectivity and complexity in fungal co-occurrence networks. The PLS-PM results reveal that soil properties, fungal diversity, and co-occurrence network complexity directly and positively drive changes in SMF. Furthermore, soil properties exert an indirect influence on SMF through their impact on fungal diversity, species composition, and network complexity. The findings of this study highlight the significant role of mixed Eucalyptus and native broadleaf plantations in enhancing SMF through improved soil properties, fungal diversity, and co-occurrence network complexity. This indicates that incorporating native broadleaf species into Eucalyptus plantations can effectively mitigate the negative impacts of monoculture plantations on soil health and ecosystem functionality. In conclusion, our study contributes to the understanding of how mixed plantations influence SMF, offering new insights into the optimization of forest management and ecological restoration strategies in artificial forest ecosystems.

An assessment of the species diversity and disease potential of Pythium communities in Europe

Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42-), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42- levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Phosphorus addition increases stability and complexity of co-occurrence network of soil microbes in an artificial Leymus chinensis grassland

Introduction

Understanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems.

Methods

In this study, the effects of four phosphorus concentrations, P0 (0 kg P ha-1), P1 (15.3 kg P ha-1), P2 (30.6 kg P ha-1), and P3 (45.9 kg P ha-1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region.

Results and discussion

The results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.

Effects of plant diversity, soil microbial diversity, and network complexity on ecosystem multifunctionality in a tropical rainforest

Introduction

Plant diversity and soil microbial diversity are important driving factors in sustaining ecosystem multifunctionality (EMF) in terrestrial ecosystems. However, little is known about the relative importance of plant diversity, soil microbial diversity, and soil microbial network complexity to EMF in tropical rainforests.

Methods

This study took the tropical rainforest in Xishuangbanna, Yunnan Province, China as the research object, and quantified various ecosystem functions such as soil organic carbon stock, soil nutrient cycling, biomass production, and water regulation in the tropical rainforest to explore the relationship and effect of plant diversity, soil microbial diversity, soil microbial network complexity and EMF.

Results

Our results exhibited that EMF decreased with increasing liana species richness, soil fungal diversity, and soil fungal network complexity, which followed a trend of initially increasing and then decreasing with soil bacterial diversity while increasing with soil bacterial network complexity. Soil microbial diversity and plant diversity primarily affected soil nutrient cycling. Additionally, liana species richness had a significant negative effect on soil organic carbon stocks. The random forest model suggested that liana species richness, soil bacterial network complexity, and soil fungal network complexity indicated more relative importance in sustaining EMF. The structural equation model revealed that soil bacterial network complexity and tree species richness displayed the significantly positive effects on EMF, while liana species richness significantly affected EMF via negative pathway. We also observed that soil microbial diversity indirectly affected EMF through soil microbial network complexity. Soil bulk density had a significant and negative effect on liana species richness, thus indirectly influencing EMF. Simultaneously, we further found that liana species richness was the main indicator of sustaining EMF in a tropical rainforest, while soil bacterial diversity was the primary driving factor.

Discussion

Our findings provide new insight into the relationship between biodiversity and EMF in a tropical rainforest ecosystem and the relative contribution of plant and soil microibal diversity to ecosystem function with increasing global climate change.

Non-rhizobial nodule endophytes improve nodulation, change root exudation pattern and promote the growth of lentil, for prospective application in fallow soil

Non-rhizobial endophytes (NREs) are active colonizers inhabiting the root nodules. Though their active role in the lentil agroecosystem is not well defined, here we observed that these NREs might promote the growth of lentils, modulate rhizospheric community structure and could be used as promising organisms for optimal use of rice fallow soil. NREs from root nodules of lentils were isolated and examined for plant growth-promoting traits, exopolysaccharide (EPS) and biofilm production, root metabolites, and the presence of nifH and nifK elements. The greenhouse experiment with the chosen NREs, i.e., Serratia plymuthica 33GS and Serratia sp. R6 significantly increased the germination rate, vigour index, development of nodules (in non-sterile soil) and fresh weight of nodules (33GS 94%, R6 61% growth) and length of the shoot (33GS 86%, R6 51.16%) as well as chlorophyll levels when compared to the uninoculated control. Scanning Electron Microscopy (SEM) revealed that both isolates could successfully colonize the roots and elicit root hair growth. The inoculation of the NREs resulted in specific changes in root exudation patterns. The plants with 33GS and R6 treatment significantly stimulated the exudation of triterpenes, fatty acids, and their methyl esters in comparison to the uninoculated plants, altering the rhizospheric microbial community structure. Proteobacteria dominated the rhizospheric microbiota in all the treatments. Treatment with 33GS or R6 also enhanced the relative abundance of other favourable microbes, including Rhizobium, Mesorhizobium, and Bradyrhizobium. The correlation network analysis of relative abundances resulted in numerous bacterial taxa, which were in cooperation with each other, having a possible role in plant growth promotion. The results indicate the significant role of NREs as plant growth promoters, which also includes their role in root exudation patterns, enhancement of soil nutrient status and modulation of rhizospheric microbiota, suggesting their prospects in sustainable, and bio-based agriculture.