Distinct rhizosphere effect on active and total bacterial communities in paddy soils

Enhancing carrot (Daucus carota var. sativa Hoffm.) plant productivity with combined rhizosphere microbial consortium

Background

Plant growth-promoting rhizobacteria (PGPR) are an integral part of agricultural practices due to their roles in promoting plant growth, improving soil conditions, and suppressing diseases. However, researches on the PGPR in the rhizosphere of carrots, an important vegetable crop, is relative limited. Therefore, this study aimed to isolate and characterize PGPR strains from the rhizosphere soil of greenhouse-grown carrots, with a focus on their potential to stimulate carrot growth.

Methods

Through a screening process, 12 high-efficiency phosphorus-solubilizing bacteria, one nitrogen-fixing strain, and two potassium-solubilizing strains were screened. Prominent among these were Bacillus firmus MN3 for nitrogen fixation ability, Acinetobacter pittii MP41 for phosphate solubilization, and Bacillus subtilis PK9 for potassium-solubilization. These strains were used to formulate a combined microbial consortium, N3P41K9, for inoculation and further analysis.

Results

The application of N3P41K9, significantly enhanced carrot growth, with an increase in plant height by 17.1% and root length by 54.5% in a pot experiment, compared to the control group. This treatment also elevated alkaline-hydrolyzable nitrogen levels by 72.4%, available phosphorus by 48.2%, and available potassium by 23.7%. Subsequent field trials confirmed the efficacy of N3P41K9, with a notable 12.5% increase in carrot yields. The N3P41K9 treatment had a minimal disturbance on soil bacterial diversity and abundance, but significantly increased the prevalence of beneficial genera such as Gemmatimonas and Nitrospira. Genus-level redundancy analysis indicated that the pH and alkali-hydrolyzable nitrogen content were pivotal in shaping the bacterial community composition.

Discussion

The findings of this study highlight the feasibility of combined microbial consortium in promoting carrot growth, increasing yield, and enriching the root environment with beneficial microbes. Furthermore, these results suggest the potential of the N3P41K9 consortium for soil amelioration, offering a promising strategy for sustainable agricultural practices.

Niche-specification of aerobic 2,4-dichlorophenoxyacetic acid biodegradation by tfd-carrying bacteria in the rice paddy ecosystem

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfd-mediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D.

Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng

The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng.

The isolation and identification of Bacillus velezensis ZN-S10 from vanilla (V. planifolia), and the microbial distribution after the curing process

The market value of vanilla beans (Vanilla planifolia) is constantly increasing due to their natural aroma and flavor properties that improve after a curing process, where bacteria colonization plays a critical role. However, a few publications suggest that bacteria play a role in the curing process. Hence, this study aimed to isolate Bacillus sp. that could be used for fermenting V. planifolia while analyzing their role in the curing process. Bacillus velezensis ZN-S10 identified with 16S rRNA sequencing was isolated from conventionally cured V. planifolia beans. A bacteria culture solution of B. velezensis ZN-S10 (1 mL of 1 × 107 CFU mL-1) was then coated on 1 kg of non-cured vanilla pods that was found to ferment and colonize vanilla. PCA results revealed distinguished bacterial communities of fermented vanilla and the control group, suggesting colonization of vanilla. Phylogenetic analysis showed that ZN-S10 was the dominant Bacillus genus member and narrowly correlated to B. velezensis EM-1 and B. velezensis PMC206-1, with 78% and 73% similarity, respectively. The bacterial taxonomic profiling of cured V. planifolia had a significant relative abundance of Firmicutes, Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes phyla according to the predominance. Firmicutes accounted for 55% of the total bacterial sequences, suggesting their colonization and effective fermentation roles in curing vanilla.

Soil exposure modulates the immune response to an influenza challenge in a mouse model

There is increasing evidence that early life microbial exposure aids in immune system maturation, more recently known as the "old friends" hypothesis. To test this hypothesis, 4-week-old mice were exposed to soils of increasing microbial diversity for four weeks followed by an intranasal challenge with either live or heat inactivated influenza A virus and monitored for 7 additional days. Perturbations of the gut and lung microbiomes were explored through 16S rRNA amplicon sequencing. RNA-sequencing was used to examine the host response in the lung tissue through differential gene expression. We determined that compared to the gut microbiome, the lung microbiome is more susceptible to changes in beta diversity following soil exposure with Lachnospiraceae ASVs accounting for most of the differences between groups. While several immune system genes were found to be significantly differentially expressed in lung tissue due to soil exposures, there were no differences in viral load or weight loss. This study shows that exposure to diverse microbial communities through soil exposure alters the gut and lung microbiomes resulting in differential expression of specific immune system related genes within the lung following an influenza challenge.

Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing

Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.

Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary

In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.

Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects

Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.

Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects

Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.

Effect of different types of biochar on soil properties and functional microbial communities in rhizosphere and bulk soils and their relationship with CH4 and N2O emissions

Biochar as an agricultural soil amendment plays vital roles in mediating methane (CH4) and nitrous oxide (N2O) emissions in soils. The link between different types of biochar, bulk soil, and rhizosphere microbial communities in relation to CH4 and N2O emissions is being investigated in this study. The rice pot experiment was conducted using biochar at two temperatures (300°C and 500°C) in combination with three biochar levels (0, 2, 10% w/w). Soil properties and the abundance of genes associated with CH4 and N2O emissions from both rhizosphere and bulk soils were investigated. The study also aimed to examine the structure of microbial communities (pmoA, nosZ) in rhizosphere and bulk soils whereas CH4 and N2O emissions were monitored while growing rice. Results showed that biochar at 300°C and 10% incorporation significantly increased the CH4 emissions by up to 59% rise compared to the control group. Random Forest analysis revealed that the ratio of mcrA/pmoA along with the abundance of mcrA from both rhizosphere and bulk soils, the abundance of AOA, TN, DOC, and the community composition of pmoA-harboring microorganisms from both bulk and rhizosphere soils were important predictors of CH4 emissions. Therefore, the ratio of mcrA/pmoA in rhizosphere soil and the abundance of AOA in bulk soil were the main factors influencing CH4 emissions. Variation Partitioning Analysis (VPA) results indicated that the effects of these factors on bulk soil were 9% of CH4 emissions variations in different treatments, which contributed more than rhizosphere soils' factors. Moreover, random forest analysis results indicated that the abundance of AOB in bulk soil was the most important predictor influencing N2O emissions. The VPA result revealed that the factors in rhizosphere soil could explain more than 28% of the variations in N2O emissions. Our study highlights that rhizosphere soil has a more significant effect than bulk soil on N2O production. Our findings further the understanding of the link between bulk and rhizosphere attributes, and their impact on CH4 and N2O emissions in paddy soils. In summary, we recommend the application of biochar at 500°C and 2% incorporation rate for agricultural production in the area.

Gut microbiota and transcriptome response of earthworms (Metaphire guillelmi) to polymyxin B exposure

Polymyxin B (PMB) has received widespread attention for its use as a last-line therapy against multidrug-resistant bacterial infection. However, the consequences of unintended PMB exposure on organisms in the surrounding environment remain inconclusive. Therefore, this study investigated the effects of soil PMB residue on the gut microbiota and transcriptome of earthworms (Metaphire guillelmi). The results indicated that the tested doses of PMB (0.01-100 mg/kg soil) did not significantly affect the richness and Shannon's diversity index of the earthworm gut microbiota, but PMB altered its community structure and taxonomic composition. Moreover, PMB significantly affected Lysobacter, Aeromonas, and Sphingomonas in the soil microbiota, whereas Pseudomonas was significantly impacted the earthworm gut microbiota. Furthermore, active bacteria responded more significantly to PMB than the total microbial community. Bacterial genera such as Acinetobacter and Bacillus were highly correlated with differential expression of some genes, including up-regulated genes associated with folate biosynthesis, sulphur metabolism, and the IL-17 signalling pathway, and downregulated genes involved in vitamin digestion and absorption, salivary secretion, other types of O-glycan biosynthesis, and the NOD-like receptor signalling pathway. These results suggest that adaptation to PMB stress by earthworms involves changes in energy metabolism, their immune and digestive systems, as well as glycan biosynthesis. The study findings help elucidate the relationship between earthworms and their microbiota, while providing a reference for understanding the environmental risks of PMB.

Root architectures differentiate the composition of organic carbon in bauxite residue during natural vegetation

Understanding plant root architectures induced changes in organic carbon accumulation and conversion is critical to predicting carbon cycling and screening appropriate plant species for ecological restoration on bauxite residue disposal areas. According to the ecological investigation of a weathered bauxite residue disposal area, three plants with different root architectures including Artemisia lavandulaefolia (A. lavandulaefolia), moss, and Zanthoxylum simulans (Z. simulans) were selected to investigate the rhizosphere effects on the composition and structure of organic carbon in bauxite residue. The physic-chemical properties, the contents and structure of different organic carbon fractions, and microbial communities of bauxite residue from rhizosphere and non-rhizosphere were analyzed. Plant growth decreased the saline-alkalinity, increased the contents of total organic carbon, particulate organic carbon and dissolved organic carbon, whilst enhancing the enzymatic activities of bauxite residue. Meanwhile, the rhizosphere effects had significant effects on the accumulation and stabilization of organic carbon in bauxite residue. A. lavandulaefolia had the strongest rhizosphere effects on the composition and structure of total organic carbon and dissolved organic carbon, whilst moss was more effective on the accumulation of particulate organic carbon in bauxite residue. Plant growth and root architecture changed the abundance of specific functional microorganisms and the complexity of microbial co-occurrence networks, thus elevating organic carbon levels in bauxite residue. During natural vegetation encroachment, rhizosphere exciting effects of the salt-tolerated plants could change the composition and structure of organic carbon fractions due to the comprehensive effectiveness of the improvement of physic-chemical properties and microbial communities. The findings improve our understanding of the responses of sequestration and stabilization of organic carbon pools to ecological restoration on bauxite residue disposal areas.

Metabolomic profiles reveals the dose-dependent effects of rice grain yield and nutritional quality upon exposure zero-valent iron nanoparticles

Zero-valent iron nanoparticles (nZVI) were widely used material in environmental remediation, which has attracted increasing concern for their safety. Previous studies have shown that the addition of nZVI could inhibit rice seedling growth. However, the effect of nZVI on the soil-rice system during the entire life cycle was not reported. Furthermore, the effect of nZVI on the quality of rice grain has also not been studied. Therefore, we investigated the effects of rice grain yield and nutritional quality upon exposure nZVI. The results showed that the soil pH value, redox potential and Fe (II) content in the nZVI-treated group were decreased in a dose-dependent manner. Interestingly, 2500 mg/kg nZVI significantly decreased the relative abundance of several functional microbial communities (10.52-73.53 %) associated with carbon and nitrogen cycles in response to plants compared to the control. Meanwhile, the nZVI treatment clearly reduced grain yield (8.71-18.21 %). Furthermore, the content of protein (51.72-57.79 %) and several essential nutrients (Zn, Cu, Mn and Mo) in the nZVI-treated grains was also decreased in a dose-dependent manner. The results of grain metabolomics indicated that nZVI could interfere with the relative expression of lysine and glutathione by regulating the metabolic pathways of antioxidant and protein synthesis in rice.

Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB

The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.

Inoculation with carbofuran-degrading rhizobacteria promotes maize growth through production of IAA and regulation of the release of plant-specialized metabolites

Toxic residues of the insecticide carbofuran in farmland is an urgent problem, and high concentrations of carbofuran have been found in the rhizoshperic soil of maize treated with seed coating agents 120-180 days after planting. Using an enrichment co-culture method, we identify a bacterial strain obtained from these carbofuran-contaminated rhizosphere soils as Leclercia adecarboxylata MCH-1. This strain exhibited a significant ability to degrade both carbofuran and 3-keto carbofuran, with total degradation of 55.6 ± 4.6% and 75.7 ± 3.4%, respectively, 24 h following start of co-culture. Further activity screening revealed that the inoculation of maize roots with L. adecarboxylata MCH-1 promoted maize seedling growth. Quantitative analysis demonstrated that this bacterial strain had the ability to synthesize the phytohormone IAA. Simultaneously, the concentration of IAA in the rhizospheric soil increased following inoculation of maize roots with L. adecarboxylata MCH-1. Moreover, the concentrations of plant specialized metabolites, including phenolics, terpenoids, and alkaloids, decreased in maize seedlings and were elevated in the rhizospheric soil after maize roots had been inoculated with the MCH-1 strain. Interestingly, the growth of the strain MCH-1 was improved by co-culture with root exudates obtained from the rhizospheric soil, specifically 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, and zealexin A₁ (ZA₁). Taken together, our results suggest that the carbofuran-degrading rhizobacterium L. adecarboxylata MCH-1 is able to interact with maize plants through the regulation of maize root exudates. Moreover, inoculation with L. adecarboxylata MCH-1 promotes maize growth through the production of IAA and regulation of the release of plant specialized metabolites. Our results provide a new model organism for the remediation of farmland soils from pollution with carbofuran residues.

Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice

Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R² ≥ 0.959, p < 0.001), followed by growth period (R² ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.

Effects of three regeneration methods on the growth and bacterial community diversity of Populus × euramericana

To study the effects of different regeneration methods on the growth and bacterial community diversity of Populus × euramericana cv. ‘74/76’ (poplar 107), we investigated the growth of poplar 107 trees under three regeneration methods in 2017 and 2020, and sequenced the 16S rDNA V5–V7 regions in stem endophytic, root endophytic, and rhizosphere soil bacteria present in samples from the three regeneration methods using the Illumina high-throughput sequencing platform. The growth analysis showed that stump grafting regeneration (ST) and stump sprouting regeneration (SP) presented similar tree height and diameter at breast height (DBH), which were significantly lower by planted seedling regeneration (CK). The high-throughput sequencing results showed that the rhizosphere soil bacteria appeared to be significantly more diverse and rich than the root and stem endophytic bacteria. Cluster analysis showed that the similarity of bacterial community structure among the rhizosphere soil, root, and stem was small. Thus, the three sample types showed significant differences in bacteria. While comparing the two years, 2020 was significantly more diverse and rich than 2017. With the increase in stand age, the abundance of Proteobacteria increased and the abundance of Acidobacteria decreased. Among the three regeneration methods, ST significantly increased the diversity of stem endophytic bacteria. Chthoniobacter was enriched in SP, which promoted the decomposition of organic matter, and more plant growth promoting rhizobacteria (PGPR) were accumulated in the rhizosphere of SP and ST. The composition of the bacterial community was similar in the three regeneration methods, but the community composition was different. Regeneration and transformation of poplar plantations can be better carried out by stump grafting and stump sprouting.

Rhizosphere and Straw Return Interactively Shape Rhizosphere Bacterial Community Composition and Nitrogen Cycling in Paddy Soil

Currently, how rice roots interact with straw return in structuring rhizosphere communities and nitrogen (N) cycling functions is relatively unexplored. In this study, paddy soil was amended with wheat straw at 1 and 2% w/w and used for rice growth. The effects of the rhizosphere, straw, and their interaction on soil bacterial community composition and N-cycling gene abundances were assessed at the rice maturity stage. For the soil without straw addition, rice growth, i.e., the rhizosphere effect, significantly altered the bacterial community composition and abundances of N-cycling genes, such as archaeal and bacterial amoA (AOA and AOB), nirK, and nosZ. The comparison of bulk soils between control and straw treatments showed a shift in bacterial community composition and decreased abundance of AOA, AOB, nirS, and nosZ, which were attributed to sole straw effects. The comparison of rhizosphere soils between control and straw treatments showed an increase in the nifH gene and a decrease in the nirK gene, which were attributed to the interaction of straw and the rhizosphere. The number of differentially abundant genera in bulk soils between control and straw treatments was 13-23, similar to the number of 16-22 genera in rhizosphere soil between control and straw treatment. However, the number of genera affected by the rhizosphere effect was much lower in soil amended with straw (3-4) than in soil without straw addition (9). Results suggest possibly more pronounced impacts of straw amendments in shaping soil bacterial community composition.

Speciation Distribution and Influencing Factors of Heavy Metals in Rhizosphere Soil of Miscanthus Floridulus in the Tailing Reservoir Area of Dabaoshan Iron Polymetallic Mine in Northern Guangdong

Through field investigation and experimental analysis, the forms, contents and distribution of heavy metals (Zn, Pb, Cu, Cd, Ni, Cr) in rhizosphere and non-rhizosphere soils of Miscanthus floridulus growing everywhere in Tielongwei mine pond (sample plot 1), Caoduikeng tailings pond (sample plot 2), Donghua tailings pond (sample plot 3) and Small tailings pond (sample plot 4) in Dabaoshan, Guangdong Province were studied. The results showed that the main forms and distributions of heavy metals in rhizosphere and non-rhizosphere soils are basically the same, which shows that the mineral content accounts for most of the total amount of heavy metals, while the exchange content is low. Compared with non-rhizosphere soil, the proportion of exchangeable and organic heavy metals in rhizosphere soil increased significantly, in which the proportion of organic-bound Cu increased by 53.25%, the proportion of organic-bound Cd and Pb increased by more than 17%, and the proportion of Zn increased by 5.67%. At the same time, the contents of carbonate-bound and iron manganese oxide-bound decreased. Statistical analyses showed that the morphological distribution of Zn, Pb, Cu, Cd, Ni and Cr in rhizosphere soil was closely related to soil pH value, organic matter content, plant growth and other factors. The results of this study provided a basis for the restoration of heavy metal-contaminated sites by Miscanthus.

Impacts of typical engineering nanomaterials on the response of rhizobacteria communities and rice (Oryza sativa L.) growths in waterlogged antimony-contaminated soils

The combined eco-risks of Sb (widely presented in soils, especially nearing mining areas) and the engineering nanomaterials (ENMs) (applied in agriculture and soil remediation) still remain uncovered. The current study investigated the impacts of single and combined exposure of CuO, CeO₂ nanoparticles (NPs) and multi-walled carbon nanotube (MWCNTs) with Sb on rice growths and rhizosphere bacterial communities. The results showed that co-exposure of CuO NPs (0.075 wt%) with Sb (III) posed the most adverse impacts on root biomass and branches (up to 66.59% and 70.00% compared to other treatments, respectively). Treatments containing MWCNTs showed insignificant dose-dependent effects, while CeO₂ NPs combined with Sb (III) showed significant synergistic stimulating effects on the fresh weights of root and shoot, by 68.30% and 73.48% (p < 0.05) compared to single Sb exposure, respectively. The rice planting increased the percentage of non-specifically sorbed Sb in soils by 1.50-14.49 than the no-planting stage. Analysis on microbial communities revealed that co-exposure of CuO NPs with Sb (III) induced the greatest adverse impacts on rhizobacteria abundances and community structures at both phylum and genus levels. Therein, significant decrease of Bacteroidetes, Acidobacteria and increase of Firmicutes abundance at the phylum level were observed. This study provided information about the risks of different ENMs released to Sb-contaminated soils under flooded condition on both crops and bacterial communities.

Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis

Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.

Dissolved organic carbon drives nutrient cycling via microbial community in paddy soil

Microbial mediated iron cycling drives the biogeochemical cycling of carbon, nitrogen, sulfur, and phosphorus. However, the fate of the microbial community and the relative metabolic pathways in paddy soil after the addition of biogas slurry are poorly understood. In this study, the response of functional genes was investigated by growing one-season rice in paddy soils in a pot experiment. Seven treatments were prepared: 1) control (CK); 2) organic carbon (OC); 3) fertilizer (F); 4) 5% of biogas slurry (B05); 5) 10% of biogas slurry (B10); 6) 15% of biogas slurry (B15); 7) 20% of biogas slurry (B20). In the biogas slurry treatments, Geobacter increased more than in the other treatments during rice growth, which were structured by TOC. Particularly, in the B10 treatment, the relative abundance of Geobacter was 1.6 and 14.8 times higher than that of CK at the heading and mature stages, respectively. At the heading stage, the addition of biogas slurry and OC shifted the microbial phosphorus-transformation communities differently. There were no significant differences in the carbon, nitrogen, and sulfur metabolic pathways between the two treatments. At the mature stage, the carbon: nitrogen: phosphorus balance was significantly influenced by the regulation of functional gene expression and metabolic activities. These findings provide insight into the key factors affecting carbon, nitrogen, sulfur, phosphorus, and iron during rice growth after carbon inputs.

Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities

Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.

Alteration and the Function of Intestinal Microbiota in High-Fat-Diet- or Genetics-Induced Lipid Accumulation

Diet and host genetics influence the composition of intestinal microbiota, yet few studies have compared the function of intestinal microbiota in the diet- or genotype-induced lipid deposition, which limits our understanding of the role of intestinal bacteria in metabolic disorders. The lipid accumulation in wild-type zebrafish fed with control (CON) or high-fat (HF) diet and two gene-knockout zebrafish lines (cpt1b^–/– or pparab^–/–) fed with control diet was measured after a 4-week feeding experiment. The intestinal microbiota composition of these groups was investigated using 16S ribosomal RNA (rRNA) gene sequencing (DNA-based) and 16S rRNA sequencing (RNA-based). The HF diet or deficiency of two genes induced more weight gain and higher triglyceride content in the liver compared with their control group. 16S rRNA gene sequencing (DNA-based) indicated the decreased abundance of Proteobacteria in the HF group compared with CON, but there was no significant difference in bacterial α diversity among treatments. 16S rRNA sequencing (RNA-based) confirmed the decreased abundance of Proteobacteria and the bacterial α diversity in the HF group compared with CON. Deficiency of cpt1b or pparab showed less change in microbiota composition compared with their wild-type group. Intestinal microbiota of each group was transferred to germ-free zebrafish, and the quantification of Nile red staining indicated that the intestinal microbiota of the HF group induced more lipid accumulation compared with CON, whereas intestinal microbiota of cpt1b^–/– and pparab^–/– zebrafish did not. The results showed that RNA-based bacterial sequencing revealed more bacterial alteration than DNA-based bacterial sequencing. HF diet had a more dominant role in shaping gut microbiota composition to induce lipid accumulation compared with the gene-knockout of cpt1b or pparab in zebrafish, and the transplant of intestinal microbiota from HF-fed fish induced more lipid deposition in germ-free zebrafish. Together, these data suggested that a high-fat diet exerted a more dominant role over the deletion of cpt1b or pparab on the intestinal bacterial composition, which corresponded to lipid accumulation.

Distinct patterns of abundant and rare subcommunities in paddy soil during wetting-drying cycles

Wetting-drying cycles typically result in a wide range of soil moistures and redox potentials (Eh) that significantly affect the soil microbial community. Although numerous studies have addressed the effects of soil moisture on soil microbial community structure and composition, the response of active microbes to the fluctuation in soil Eh is still largely unknown; this is especially true for the ecological roles of abundant and rare taxa. To explore the dynamics of active and total microbial communities in response to wetting-drying cycles, we conducted a microcosm experiment based on three wetting-drying cycles and 16S rRNA transcript (active) and 16S rRNA gene (total) amplicon sequencing. We found that both active and total microbial communities during three wetting-drying cycles were clustered according to the number of wetting-drying cycles (temporal factor) rather than soil moisture or Eh. Dynamics of the active microbial community, however, were redox dependent during the first wetting-drying cycle. In addition, rare taxa in the active microbial community exhibited more obvious differences than abundant ones during three wetting-drying cycles. Species turnover of abundant and rare taxa of total and active microbes, rather than species richness, explained the highest percentage of community variation. Rare taxa exhibited the most marked temporal turnover during three wetting-drying cycles. Members of Rhodospirillaceae were the major contributor to the resilience of abundant taxa of active microbes during the first wetting-drying cycle. Overall, these findings expand our current understanding of underlying assembly mechanisms of soil microbial communities responding to wetting-drying cycles.

Light exposure mediates circadian rhythms of rhizosphere microbial communities

Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light-dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light-dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.

Sorghum rhizosphere effects reduced soil bacterial diversity by recruiting specific bacterial species under low nitrogen stress

Rhizosphere microbiota play a pivotal role in promoting plant growth and defending against pathogens, but their responses to abiotic environmental stress remain largely elusive. Here, we investigated the influences of low-N stress on rhizosphere bacteria of six sorghum cultivars in a glasshouse experiment. The alpha diversity of bacteria (as revealed by Shannon diversity and Chao1 richness indices) was remarkably lower in rhizosphere soils than in bulk soils, and was significantly higher under low-N stress than under N addition. Principal coordinates analysis revealed that the bacterial community compositions in rhizosphere soils were clearly separated from bulk soils, and the rhizosphere soils under low-N stress or with N fertilization were clearly separated, indicating that both rhizosphere effects and N fertilization impacted the rhizosphere bacterial community. Notably, the relative abundances of beneficial bacteria such as Bacillaceae and Streptomycetaceae significantly increased in rhizosphere soils under low-N stress, which had significantly positive correlations with the sorghum N uptake. The relative abundance of Nitrosomonadaceae in rhizosphere soils was significantly lower than that in bulk soils, while the relative abundance of Rhizobiaceae showed an opposite pattern. Taken together, our results suggested that sorghum rhizosphere effects can reduce soil bacterial diversity possibly through recruiting specific bacterial species under low N stress.

Effects of different types of microbial inoculants on available nitrogen and phosphorus, soil microbial community, and wheat growth in high-P soil

Irrational application of chemical fertilizers causes soil nutrient imbalance, reduced microbial diversity, soil diseases, and other soil quality problems and is one of the main sources of non-point pollution. The application of microbial inoculant (MI) can improve the soil environment and crop growth to reduce problems caused by irrational application of chemical fertilizers. Field experiments were carried out in high-phosphorus soils to study the effects of the addition of various MIs combined with chemical fertilizers on soil properties, wheat growth, and soil microbial composition and structure. The MIs consisted of one fungal agent: Trichoderma compound agent (TC) and five bacterial agents, namely soil remediation agent (SR), anti-repeat microbial agent (AM), microbial agent (MA), plant growth-promoting rhizobacteria (PG), and biological fertilizer agent (BF). The wheat yield increased by 15.2-33.4% with the addition of MIs, and PG with Bacillus subtilis as the core microorganism had the most obvious effect on increasing the production (p < 0.05). For the entire growth period of wheat, all MIs applied significantly increased the available nitrogen (AN) (p < 0.05) but did not significantly affect the available phosphorus (AP). BF has the best effect on increasing AN in the soil. The 16S rRNA sequencing results indicated that the dominant phyla of soil bacteria were Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The addition of MIs increased the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi and decreased Proteobacteria and Bacteroidetes. The diversity of soil bacterial community (Chao1) was significantly higher in the soil added with TC than that added with BF (p < 0.05). All bacterial agents significantly enriched various genera (p < 0.05), while the fungal agent (TC) did not enrich the genera significantly. pH and AN, but not TP, were closely related to the dominant bacteria phylum in high-P soil. The application of MIs improved AN in soil, increased the wheat yield, and changed the relative abundance of the soil dominant phylum, and these changes were closely related to the type of MIs. The results provide a scientific basis for rational use of different types of MIs in high-P soil.

Root and Shoot Response to Nickel in Hyperaccumulator and Non-Hyperaccumulator Species

The soil-root interface is the micro-ecosystem where roots uptake metals. However, less than 10% of hyperaccumulators' rhizosphere has been examined. The present study evaluated the root and shoot response to nickel in hyperaccumulator and non-hyperaccumulator species, through the analysis of root surface and biomass and the ecophysiological response of the related aboveground biomass. Ni-hyperaccumulators Alyssoides utriculata (L.) Medik. and Noccaea caerulescens (J. Presl and C. Presl) F.K. Mey. and non-hyperaccumulators Alyssum montanum L. and Thlaspi arvense L. were grown in pot on Ni-spiked soil (0-1000 mg Ni kg^-1, total). Development of root surfaces was analysed with ImageJ; fresh and dry root biomass was determined. Photosynthetic efficiency was performed by analysing the fluorescence of chlorophyll a to estimate the plants' physiological conditions at the end of the treatment. Hyperaccumulators did not show a Ni-dependent decrease in root surfaces and biomass (except Ni 1000 mg kg^-1 for N. caerulescens). The non-hyperaccumulator A. montanum suffers metal stress which threatens plant development, while the excluder T. arvense exhibits a positive ecophysiological response to Ni. The analysis of the root system, as a component of the rhizosphere, help to clarify the response to soil nickel and plant development under metal stress for bioremediation purposes.

Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link

The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides

Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.

Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship

The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.

Soil metabolome correlates with bacterial diversity and co-occurrence patterns in root-associated soils on the Tibetan Plateau

Metabolites in root-zone soils mediate microbe-to-microbe interactions and govern the overall microbial community. However, how chemicals relate to diversity and co-occurrence patterns of bacterial communities in root-associated soils is still poorly understood. Here, we studied the relationships of soil metabolome with bacterial community diversity and co-occurrence patterns in root-associated soils across different land types on the Tibetan Plateau. The soil metabolome mainly encompassed a range of organic acids, and sugars and sugar derivatives, which were widely negatively correlated with bacterial alpha-diversity. Compared to the investigated environmental variables, metabolites accounted more for the variations in the Shannon diversity and bacterial community compositions. Compared to sugars, organic acids accounted more for bacterial community compositions at high taxonomic ranks, while reversed at genus and species levels. The relative abundances of some bacterial genera and metabolites were closely linked to soil types and plant genotypes. The differential compounds were significantly correlated with the distinctive bacterial taxa across land types and plant genotypes. Keystone species in co-occurrence network, such as Bradyrhizobium, Bryobacter, and Microvirga were significantly correlated with sugars and organic acids. Structural equation modeling revealed that sugar metabolism can play a crucial role in altering the bacterial community diversity. This study provides new insights into the ecological mechanism that maintains bacterial community in the root-associated soils on the Tibetan Plateau.

Environmentally Relevant-Level CeO2 NP with Ferrous Amendment Alters Soil Bacterial Community Compositions and Metabolite Profiles in Rice-Planted Soils

The environmental risks and benefits associated with the introduction of CeO₂ nanoparticle (NP) in agricultural soil must be carefully assessed. The ferrous ion is rich in rhizosphere soil of rice due to the reduction states underground. The aim of this study was to investigate the effects of environmentally relevant-level CeO₂ NP (25 mg·kg^-1) in the absence or presence of ferrous (30 mg·kg^-1) amendment on soil bacterial communities and soil metabolomics in rice-planted soil over 150 days. Results showed that CeO₂ NP exposure changed soil bacterial community compositions and soil metabolomics, and the above changes were further shifted with the ferrous amendment. Several functionally significant bacterial phyla containing Proteobacteria and Bacteroidetes abundances, which were associated with carbon and nitrogen cycling, were promoted after CeO₂ NP exposure with ferrous amendment. However, CeO₂ NP inhibited plant-growth-promoting rhizobacteria containing genera Bacillus and Arthrobacter irrespective of the presence or absence of ferrous. Among rhizosphere soil enzyme activities, cellulose activity was the most sensitive for CeO₂ NP exposure. NP decreased Firmicutes and increased Chloroflexi, Rokubacteria, and Thaumarchaeota abundances at the phylum level, which contributed to reduce soil cellulose activity. Additionally, CeO₂ NP positively or negatively affected soil pH, Ce accumulation in root, and rice physiological properties (root-POD, stem-POD). As a result, the above factors were related to the changes of Chloroflexi, Gemmatimonadetes, Rokubacteria, Thaumarchaeota, and Nitrospirae at the phylum level. After adding CeO₂ NP with ferrous or not, the main metabolic changes were concentrated on fluctuations in starch and sucrose metabolism, nitrogen metabolism, sulfur metabolism, propanoate metabolism, fatty acid metabolism, and urea cycle. The eight changed metabolites containing glycerol monstearate, boric acid, monopalmitin, palmitic acid, alkane, ethanol, dicarboximide, and stearic acid accounted for the separation of different treatments with CeO₂ NP exposure. Activities of soil enzymes (urease, invertase, and cellulose), pH, and soil organic matter affected dominant metabolites containing fatty acids, inorganic acid, and sugar. Network analysis showed that the influence of soil bacterial community on metabolites varied with metabolites and bacteria species. The presence of CeO₂ NP mainly promoted fatty acids (hexanoic acid, nonanoic acid) and amino acid (oxoproline) and amine (diethanolamine) concentrations, which could be from the increased Proteobacteria abundance after CeO₂ NP exposure. Phylum Proteobacteria had the most genus species containing 13 genera affecting soil metabolite profiles. These results provide valuable information for understanding the impact of environmentally relevant-level CeO₂ NP exposure on soil microbial communities and metabolites with or without ferrous, which is needed to understand the ecological risk posed by long-term CeO₂ NP exposure in rice-planted soil with rich ferrous.

Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh

Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.

Similar but Not Identical Resuscitation Trajectories of the Soil Microbial Community Based on Either DNA or RNA after Flooding

Both drought and flooding are unfavorable for soil microorganisms, but nevertheless, are highly relevant to the extreme weather events that have been predicted to increase in the future. The switch of soil water status from drought to flooding can happen rapidly and microbial activity might be either stimulated or further inhibited, but we have insufficient understanding of the underlying microbial processes. Here, we tracked the changes in soil bacterial and fungal abundance and their community structures, assaying the total (DNA-based) and potentially active (RNA-based) communities in response to abrupt flooding of dry soil. Also, rates of soil respiration and enzyme activity were measured after flooding. Results showed that the bacterial community was found to be more responsive than the fungal community to flooding. The bacterial community responses were clearly classified into three distinct patterns in which the intermediate pattern displayed highly phylogenetic clustering. A transient flourish of Bacilli which belongs to Firmicutes was detected at 8–48 h of flooding, suggesting its potential importance in the microbial assemblage and subsequent ecosystem functioning. Finally, the accumulative amount of CO2 released was more closely related than enzyme activity to the change in structure of the bacterial community after flooding. In conclusion, these findings extended our understanding of the underlying soil microbial processes following abrupt water condition changes.

Bacterial Diversity and Community Structure in Typical Plant Rhizosphere

Bacteria play a vital role in the quality of soil, health, and the production of plants. This has led to several studies in understanding the diversity and structure in the plant rhizosphere. Over the years, there have been overwhelming advances in molecular biology which have led to the development of omics techniques which utilize RNA, DNA, or proteins as biomolecules; these have been gainfully used in plant–microbe interactions. The bacterial community found in the rhizosphere is known for its colonization around the roots due to availability of nutrients, and composition, and it affects the plant growth directly or indirectly. Metabolic fingerprinting enables a snapshot of the metabolic composition at a given time. We review metabolites with ample information on their benefit to plants and which are found in rhizobacteria such as Pseudomonas spp. and Bacillus spp. Exploring plant-growth-promoting rhizobacteria using omics techniques can be a true success story for agricultural sustainability.

DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors

Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%–40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.

RNA Stable Isotope Probing of Potential Feammox Population in Paddy Soil

Anaerobic ammonium oxidation coupled to iron reduction (Feammox) is a recently discovered pathway contributing to nitrogen loss in various ecosystems such as paddy soils and sediments. However, little is known about the microbes driving Feammox in an agricultural ecosystem. Here, we demonstrated the occurrence of Feammox in paddy soils of Southern China using a ¹⁵N isotopic tracing technique, and examined the microbial communities associated with Feammox using RNA based stable isotope probing (RNA-SIP) combined with Illumina sequencing. Feammox was detected in all collected soils with direct N₂ production as the dominant Feammox pathway. It was estimated that approximately 6.91% of the applied nitrogen fertilizers were lost through Feammox in the paddy soils. RNA-SIP results showed that the composition of enriched active microbial communities were dependent on soil properties, especially the soil pH and grain size. Geobacter were enriched in most soils across various properties. The abundance of enriched GOUTA19 were significantly higher in soils with low pH than those in soils with medium pH and high pH, and the relative abundance of active Nitrososphaeraceae and Pseudomonas only increased in soils with medium and high pH during 4-day of incubation. These results suggested Feammox is a ubiquitous and important process for N loss. Geobacter, GOUTA19, Nitrososphaeraceae and Pseudomonas were active during the incubation that favored Feammox and the growth of Feammox microbes, suggesting these microbes were potentially associated with Feammox in natural agricultural soils.