Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia)

An inclusive study to elucidation the heavy metals-derived ecological risk nexus with antibiotic resistome functional shape of niche microbial community and their carbon substrate utilization ability in serpentine soil

Heavy metals (HMs) contained terrestrial ecosystems are often significantly display the antibiotic resistome in the pristine area due to increasing pressure from anthropogenic activity, is complex and emerging research interest. This study investigated that impact of chromium (Cr), nickel (Ni), cobalt (Co) concentrations in serpentine soil on the induction of antibiotic resistance genes and antimicrobial resistance within the native bacterial community as well as demonstrated their metabolic fingerprint. The full-length 16S-rRNA amplicon sequencing observed an increased abundance of Firmicutes, Actinobacteriota, and Acidobacteriota in serpentine soil. The microbial community in serpentine soil displayed varying preferences for different carbon sources, with some, such as carbohydrates and carboxylic acids, being consistently favored. Notably, 27 potential antibiotic resistance opportunistic bacterial genera have been identified in different serpentine soils. Among these, Lapillicoccus, Rubrobacter, Lacibacter, Chloroplast, Nitrospira, Rokubacteriales, Acinetobacter, Pseudomonas were significantly enriched in high and medium HMs concentrated serpentine soil samples. Functional profiling results illustrated that vancomycin resistance pathways were prevalent across all groups. Additionally, beta-lactamase, aminoglycoside, tetracycline, and vancomycin resistance involving specific bio-maker genes (ampC, penP, OXA, aacA, strB, hyg, aph, tet(A/B), otr(C), tet(M/O/Q), van(A/B/D), and vanJ) were the most abundant and enriched in the HMs-contaminated serpentine soil. Overall, this study highlighted that heavy-metal enriched serpentine soil is potential to support the proliferation of bacterial antibiotic resistance in native microbiome, and might able to spread antibiotic resistance to surrounding environment.

Rhizosphere microbiome of plants used in phytoremediation of mine tailing dams

Rhizospheric microbial communities improve the effectiveness of hyperaccumulators in the phytoremediation of heavy metals. However, limited access to tailing dams and inadequate assessment of plants' phytoremediation potential limit the characterization of native accumulators, hindering the effectiveness of local remediation efforts. This study evaluates the heavy metal sequestration potentials of Pennisetum purpureum, Leucaena leucocephala, and Pteris vittata and their associated rhizospheric microbial communities at the Marlu and Pompora tailing dams in Ghana. The results indicate shoot hyperaccumulation of Cd (334.5 ± 6.3 mg/kg) and Fe (10,647.0 ± 12.6 mg/kg) in P. purpureum and L. leucocephala, respectively. Analysis of rhizospheric bacterial communities revealed the impact of heavy metal contamination on bacterial community composition, associating Fe and Cd hyperaccumulation with Bacillus, Arthrobacter, and Sphingomonas species. This study reports the hyperaccumulation potentials of L. leucocephala and P. purpureum enhanced by associated rhizosphere bacterial communities, suggesting their potential application as an environmentally friendly remediation process of heavy metals contaminated lands.

Physiological tolerance of black locust (Robinia pseudoacacia L.) and changes of rhizospheric bacterial communities in response to Cd and Pb in the contaminated soil

Woody plants possess great potential for phytoremediation of heavy metal-contaminated soil. A pot trial was conducted to study growth, physiological response, and Cd and Pb uptake and distribution in black locust (Robinia pseudoacacia L.), as well as the rhizosphere bacterial communities in Cd and Pb co-contaminated soil. The results showed that R. pseudoacacia L. had strong physiological regulation ability in response to Cd and Pb stress in contaminated soil. The total chlorophyll, malondialdehyde (MDA), soluble protein, and sulfhydryl contents, as well as antioxidant enzymes (superoxide dismutase, peroxidase, catalase) activities in R. pseudoacacia L. leaves under the 40 mg·kg-1 Cd and 1000 mg·kg-1 Pb co-contaminated soil were slightly altered. Cd uptake in R. pseudoacacia L. roots and stems increased, while the Pb content in the shoots of R. pseudoacacia L. under the combined Cd and Pb treatments decreased in relative to that in the single Pb treatments. The bacterial α-diversity indices (e.g., Sobs, Shannon, Simpson, Ace, and Chao) of R. pseudoacacia L. rhizosphere soil under Cd and Pb stress were changed slightly relative to the CK treatment. However, Cd and Pb stress could significantly (p < 0.05) alter the rhizosphere soil microbial communities. According to heat map and LEfSe (Linear discriminant analysis Effect Size) analysis, Bacillus, Sphingomonas, Terrabacter, Roseiflexaceae, Paenibacillus, and Myxococcaceae at the genus level were notably (p < 0.05) accumulated in the Cd- and/or Pb-contaminated soil. Furthermore, the MDA content was notably (p < 0.05) negatively correlated with the relative abundances of Isosphaeraceae, Gaiellales, and Gemmatimonas. The total biomass of R. pseudoacacia L. was positively (p < 0.05) correlated with the relative abundances of Xanthobacteraceae and Vicinamibacreraceae. Network analysis showed that Cd and Pb combined stress might enhance the modularization of bacterial networks in the R. pseudoacacia L. rhizosphere soil. Thus, the assembly of the soil bacterial communities in R. pseudoacacia L. rhizosphere may improve the tolerance of plants in response to Cd and/or Pb stress.

Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain

Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.

The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale

Soils harbor some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. Numerous parameters, intrinsic to plant physiology, life history and the soil itself, can influence the structure of rhizomicrobial communities. While our knowledge of rhizosphere microbial diversity is increasing, opinion is divided as to whether the factors that most impact this diversity are abiotic, climatic or plant selection. Here we focused on the rhizosphere bacterial diversity of nickel hyperaccumulator plants (28 species from Mediterranean or tropical climates). We showed, by leveraging 16S Illumina sequencing of 153 ultramafic rhizosphere soils, that bacterial genetic diversity was highest in Mediterranean habitats where plant diversity was the lowest. Concerning those parameters driving this diversity, we demonstrated that climate drives bacterial diversity, in particular with the annual temperature variation. Focusing on each region, we underlined the substantial role of soil physicochemical parameters. Our results highlight the importance of considering spatial scale when explaining bacterial community diversity.

Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests

Depending on their tree species composition, forests recruit different soil microbial communities. Likewise, the vertical nutrient gradient along soil profiles impacts these communities and their activities. In forest soils, bacteria and fungi commonly compete, coexist, and interact, which is challenging for understanding the complex mechanisms behind microbial structuring. Using amplicon sequencing, we analyzed bacterial and fungal diversity in relation to forest composition and soil depth. Moreover, employing random forest models, we identified microbial indicator taxa of forest plots composed of either deciduous or evergreen trees, or their mixtures, as well as of three soil depths. We expected that forest composition and soil depth affect bacterial and fungal diversity and community structure differently. Indeed, relative abundances of microbial communities changed more across soil depths than in relation to forest composition. The microbial Shannon diversity was particularly affected by soil depth and by the proportion of evergreen trees. Our results also reflected that bacterial communities are primarily shaped by soil depth, while fungi were influenced by forest tree species composition. An increasing proportion of evergreen trees did not provoke differences in main bacterial metabolic functions, e.g., carbon fixation, degradation, or photosynthesis. However, significant responses related to specialized bacterial metabolisms were detected. Saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi were related to the proportion of evergreen trees, particularly in topsoil. Prominent microbial indicator taxa in the deciduous forests were characterized to be r-strategists, whereas K-strategists dominated evergreen plots. Considering simultaneously forest composition and soil depth to unravel differences in microbial communities, metabolic pathways and functional guilds have the potential to enlighten mechanisms that maintain forest soil functionality and provide resistance against disturbances.

Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils

Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.

Stochastic processes shape the biogeographic variations in core bacterial communities between aerial and belowground compartments of common bean

Although studies of biogeography in soil bacterial communities have attracted considerable attention, the generality of these patterns along with assembly processes and underlying drivers is poorly understood in the inner tissues of plants. Plant tissues provide unique ecological habitats for microorganisms, which play an essential role in plant performance. Here, we compared core bacterial communities among five soil-plant associated compartments of common bean across five sampling sites in China. Neutral and null modelling consistently suggested that stochastic processes dominated the core community assembly processes and escalated from the belowground compartments to the inner tissues of aerial plant parts. The multiple distance-decay relationships also varied and had flattened patterns in the stem endosphere, which were shaped by distinct environmental factors in each compartment. Coexistence patterns also varied in topological features, in addition with the sparsest networks in the stem endosphere resulted from the interaction with the stochastic processes. This study considerably expanded our understanding of various biogeographic patterns, assembly processes, and the underlying mechanisms of core bacterial communities between aerial and belowground compartments of common bean. That will provide a scientific basis for the reasonable regulation of core bacterial consortia to get better plant performance.