Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

Metagenomic insights to bacterial communities, functional traits, and soil health in banana smallholder agroecosystems of Kenya

Microbes inhabiting the banana rhizosphere are varied and mediate essential functions that enhance plant growth and increase crop productivity. Their abundance in soil habitats is a potential indicator of soil health and quality. Despite the well-known benefits of rhizosphere microorganisms in banana cultivation, their genomic and functional diversity remains largely unexplored within smallholder agroecosystems. In this study, we characterized the community composition and functional potential of bacteria in banana rhizospheric soils from Gituamba, Mangu and Ngenda constituencies in Kiambu County, Kenya. Using Illumina Novaseq sequencing, we analyzed 16S rRNA gene amplicons and shotgun metagenomic profiles to explore these microbial communities. Variations of soil physicochemical parameters across the study sites were assessed. The parameters varied across the sites, with soils in Gituamba and Ngenda depicting better soil fertility characteristics than Mangu. Amplicon sequencing profiles revealed higher bacterial diversity in Gituamba compared to Mangu, while the single sample from Ngenda exhibited moderate diversity. The dominant phyla across the study sites were Proteobacteria, Actinobacteria, and Cyanobacteria. Functional profiling of 16S rRNA gene amplicons showed a higher enrichment in Gituamba compared to Mangu. Overall, the functional profiling indicated that predicted metabolic pathways across the study sites were linked to genes encoded by the members of the most abundant bacterial phyla in the soil environments, majorly contributing to beneficial roles for soil health and crop yield. This study offers methods to reveal the banana rhizosphere as a rich reservoir for potential microbes of agricultural and biotechnological significance, which can promote sustainable agriculture.

Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation

The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.

Deciphering the mechanism of rhizosphere microecosystem in modulating rice cadmium accumulation via integrating metabolomics and metagenomics

Cadmium (Cd) accumulation in rice poses significant risks to human health. The Cd accumulation levels vary widely among cultivars and are strongly associated with the rhizosphere microecosystem. However, the underlying mechanisms remain poorly understood. Here, we conducted a field experiment in Cd-contaminated areas with 24 popular regional cultivars. These cultivars were categorized into high Cd accumulation (HA) and low Cd accumulation (LA) groups based on their grain Cd content. Rhizosphere soil physicochemical properties were monitored, and key metabolites, microbiomes, and their interaction contributing to Cd accumulation were analyzed using omics-sequencing technologies and bioinformatics analysis. Metabolomic analysis identified distinct rhizosphere metabolite profiles between the HA and LA groups, with key metabolites showing strong correlations with Cd accumulation. Key metabolites in the LA group were linked to reduced Cd uptake and enhanced antioxidant defense mechanisms, while those in the HA group were associated with increased Cd mobility and uptake. Metagenomic analysis of the rhizosphere soil showed that the LA group harbored a more diverse and interconnected microbial community, with tax such as Syntrophaceae, Anaerolineae, Thermoflexales, and Syntrophales, along with metabolite such as disopyramide, playing central roles in Cd immobilization and detoxification. Additionally, the enhanced carbon, nitrogen, and phosphorus cycling in the LA group suggests a more robust nutrient assimilation process that supports plant growth and reduces Cd uptake. This study highlights the critical role of the rhizosphere microecosystem in regulating Cd accumulation and underscores the potential of selecting rice cultivars with favorable rhizosphere traits as a strategy for reducing Cd uptake.

Whole genome analysis of Bacillus velezensis 160, biological control agent of corn head smut

Corn head smut is a disease caused by the fungus Sporisorium reilianum. This phytosanitary problem has existed for several decades in the Mezquital Valley, an important corn-producing area in central Mexico. To combat the problem, a strain identified as Bacillus subtilis 160 was applied in the field, where it decreased disease incidence and increased crop productivity. In this study, the sequencing and analysis of the whole genome sequence of this strain were carried out to identify its genetic determinants for the production of antimicrobials. The B. subtilis 160 strain was found to be Bacillus velezensis. Its genome has a size of 4,297,348 bp, a GC content of 45.8%, and 4,174 coding sequences. Comparative analysis with the genomes of four other B. velezensis strains showed that they share 2,804 genes and clusters for the production of difficidin, bacillibactin, bacilysin, macrolantin, bacillaene, fengycin, butirosin A, locillomycin, and surfactin. For the latter metabolite, unlike the other strains that have only one cluster, B. velezensis 160 has three. A cluster for synthesizing laterocidine, an antimicrobial reported only in Brevibacillus laterosporus, was also identified.

IMPORTANCE

In this study, we performed sequencing and analysis of the complete genome of the strain initially identified as Bacillus subtilis 160 as part of its characterization. This bacterium has shown its ability to control corn head smut in the field, a disease caused by the basidiomycete fungus Sporisorium reilianum. Analyzing the complete genome sequence not only provides a more precise taxonomic identification but also sheds light on the genetic potential of this bacterium, especially regarding mechanisms that allow it to exert biological control. Employing molecular and bioinformatics tools in studying the genomes of agriculturally significant microorganisms offers insights into the development of biofungicides and bioinoculants. These innovations aim to enhance plant growth and pave the way for strategies that boost crop productivity.

Deciphering the spatial distribution and function profiles of soil bacterial community in Liao River estuarine wetland, Northeast China

Soil microbes play vital roles in estuarine wetlands. Understanding the soil bacterial community structure and function profiles is essential to reveal the ecological functions of microbes in estuarine wetlands. Herein, soil samples were collected from Liao River estuarine wetland, Northeast China, along the river to the estuarine mouth, and soil bacterial communities were explored. Results showed that soil physiochemical properties, bacterial community structure and functions exhibited distinct variations influenced by geographical location. Bacterial phyla in soils were dominated by Proteobacteria and Bacteroidetes, while Gillisia and Woeseia were the predominant genera. Soil pH, electrical conductivity and nitrogen-related nutrients were the important factors affecting bacterial community structure. Based on PICRUSt prediction, the genes related to metabolism of nitrogen, sulfur and methane showed spatial distribution patterns, and the abundances of most biomarker genes increased as the distance from estuarine mouth extended. These findings could enrich the understanding of soil microbiome in estuarine wetlands.

Genotypic variation in grain cadmium concentration in wheat: Insights into soil pollution, agronomic characteristics, and rhizosphere microbial communities

Soil cadmium (Cd) pollution poses a serious threat to both the productivity and quality of wheat. This study aimed to investigate the genotypic variation in grain Cd concentration in wheat through field and pot experiments. Among 273 wheat genotypes, a significant genotypic difference was found in grain Cd concentration, ranging from 0.01 to 0.14 mg kg-1. Two contrasting genotypes, X321 (a low grain Cd accumulator) and X128 (a high grain Cd accumulator), were selected for pot experiments. X321 exhibited a 17.9% greater reduction in yield and a 10.2% lower shoot-to-grain Cd translocation rate than X128 under Cd treatment. Grain Cd content showed a positive correlation with soil available Cd content and a negative correlation with Cu content. Soil catalase activity significantly decreased in X128 under Cd stress, whereas no difference was found in X321. The grains of X321 exhibited a more compact spatial distribution of starch grains and protein matrix than those of X128. Moreover, the size of A-type starch in X128 was larger than in X321. Meanwhile, X128 contained much B-type starch, with some surface pits observed on A-type granules under Cd stress. Cd treatment increased the abundance of rhizosphere microorganism communities, with Ellin6067 and Ramlibacter being enriched in X128 under Cd treatment, which might facilitate Cd uptake. The accumulation of Cd in grains demonstrated a strong positive correlation with the rhizosphere bacterial diversity (correlation coefficient = 0.78). These findings provide new insights into the basis of grain Cd accumulation in wheat and have potential implications for developing new verities with low Cd accumulation to ensure food safety and minimize human exposure.

Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes

Introduction

Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP).

Methods

Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing.

Results

Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms.

Conclusion

Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.

MarR Family Transcriptional Regulators and Their Roles in Plant-Interacting Bacteria

The relationship between plants and associated soil microorganisms plays a major role in ecosystem functioning. Plant-bacteria interactions involve complex signaling pathways regulating various processes required by bacteria to adapt to their fluctuating environment. The establishment and maintenance of these interactions rely on the ability of the bacteria to sense and respond to biotic and abiotic environmental signals. In this context, MarR family transcriptional regulators can use these signals for transcriptional regulation, which is required to establish adapted responses. MarR-like transcriptional regulators are essential for the regulation of the specialized functions involved in plant-bacteria interactions in response to a wide range of molecules associated with the plant host. The conversion of environmental signals into changes in bacterial physiology and behavior allows the bacteria to colonize the plant and ensure a successful interaction. This review focuses on the mechanisms of plant-signal perception by MarR-like regulators, namely how they (i) allow bacteria to cope with the rhizosphere and plant endosphere, (ii) regulate the beneficial functions of Plant-Growth-Promoting Bacteria and (iii) regulate the virulence of phytopathogenic bacteria.

Sulfur fertilization and water management ensure phytoremediation coupled with argo-production by mediating rhizosphere microbiota in the Oryza sativa L.-Sedum alfredii Hance rotation system

Sulfur (S) fertilizers, water management and crop rotation are important agronomic practices, related to soil heavy metal bioavailability. However, the mechanisms of microbial interactions remain unclear. Herein, we investigated how S fertilizers (S⁰ and Na₂SO₄) and water management affected plant growth, soil cadmium (Cd) bioavailability, and rhizospheric bacterial communities in the Oryza sativa L. (rice)-Sedum alfredii Hance (S. alfredii) rotation system through 16S rRNA gene sequencing and ICP-MS analysis. During rice cultivation, continuous flooding (CF) was better than alternating wetting and drying (AWD). CF treatment decreased soil Cd bioavailability by the promotion of insoluble metal sulfide production and soil pH, thus lowering Cd accumulation in grains. S application recruited more S-reducing bacteria in the rhizosphere of rice, whilst Pseudomonas promoted metal sulfide production and rice growth. During S. alfredii cultivation, S fertilizer recruited S-oxidizing and metal-activating bacteria in the rhizosphere. Thiobacillus may oxidize metal sulfides and enhance Cd and S absorption into S. alfredii. Notably, S oxidation decreased soil pH and elevated Cd content, thereby promoting S. alfredii growth and Cd absorption. These findings showed rhizosphere bacteria were involved in Cd uptake and accumulation in the rice-S. alfredii rotation system, thus providing useful information for phytoremediation coupled with argo-production.

Green Manures Alter Taxonomic and Functional Characteristics of Soil Bacterial Communities

Incorporation of plant biomass into soil as green manures can reduce soilborne diseases and improve crop and soil health in agricultural ecosystems. Soil microbial communities can mediate beneficial effects of these amendments, but their response to different types of green manures is poorly understood. This study tested the effect of green manures from broccoli, marigold, and sudangrass on taxonomic and functional characteristics of soil bacterial communities. Green manures were amended to field soil and maintained in microcosms artificially infested with the soilborne plant pathogen Verticillium dahliae. Lettuce seedlings were transplanted into green manure amended and fallow soil and maintained under growth chamber conditions for 12 weeks. Bacterial communities in bulk and rhizosphere soils were characterized using nanopore sequencing of 16S rRNA and shotgun metagenome libraries. Under microcosm conditions, all green manures reduced the abundance of the soilborne plant pathogen V. dahliae and altered the taxonomic composition of bacterial communities. Twelve weeks following amendment, green manures had differential effects on lettuce yield as well as the taxonomic diversity and composition of soil bacterial communities. In addition, multiple green manures increased the abundance of bacterial functional traits in rhizosphere soil related to iron and polysaccharide acquisition and decreased the abundance of functional traits related to bacterial protein secretion systems. This study demonstrates green manures alter the taxonomic composition and functional traits in soil bacterial communities suggesting these changes may impact beneficial effects of green manures on plant and soil health.

Prevalence and mobility of integrative and conjugative elements within a Streptomyces natural population

Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we used in silico and experimental approaches on a set of 11 very closely related strains isolated from a millimeter scale rhizosphere population. Through bioinformatic searches of canonical conjugation proteins, we showed that AICEs are the most frequent integrative conjugative elements, with the central chromosome region being a hotspot for integrative element insertion. Strains exhibited great variation in AICE composition consistent with frequent HGT and/or gene loss. We found that single insertion sites can be home to different elements in different strains (accretion) and conversely, elements belonging to the same family can be found at different insertion sites. A wide variety of cargo genes was present in the AICEs with the potential to mediate strain-specific adaptation (e.g., DNA metabolism and resistance genes to antibiotic and phages). However, a large proportion of AICE cargo genes showed hallmarks of pseudogenization, consistent with deleterious effects of cargo genes on fitness. Pock assays enabled the direct visualization of conjugal AICE transfer and demonstrated the transfer of AICEs between some, but not all, of the isolates. Multiple AICEs were shown to be able to transfer during a single mating event. Although we did not obtain experimental evidence for transfer of the sole chromosomal ICE in this population, genotoxic stress mediated its excision from the chromosome, suggesting its functionality. Our results indicate that AICE-mediated HGT in Streptomyces populations is highly dynamic, with likely impact on strain fitness and the ability to adapt to environmental change.

Phytoremediation of cadmium-contaminated sediment using Hydrilla verticillata and Elodea canadensis harbor two same keystone rhizobacteria Pedosphaeraceae and Parasegetibacter

Aquatic macrophytes have been widely employed for in-situ phytoremediation of cadmium (Cd) polluted sediments. But, little is known about the responses of rhizosphere bacteria and their interspecific interactions to phytoremediation. In this study, the α-diversity, community composition, co-occurrence network and keystone species of sediment bacteria in rhizosphere zones of two typical macrophytes, Hydrilla verticillata and Elodea canadensis, were investigated using 16S rRNA gene high-throughput sequencing. The results showed that after fifty days of phytoremediation, a group of specialized sediment bacteria were assembled in the rhizosphere zones closely associated with different host macrophytes. Rhizosphere micro-environments, i.e., the increases of redox potential and organic matter and the decreases of pH, nitrogen and phosphorus, reduced bacterial α-diversity through niche-based species-sorting process, which in turn reduced interspecific mutualistic relationships. But meanwhile, benefiting from the nutrients supplied from macrophyte roots, more bacterial species survived in the highly Cd-contaminated sediments (50 mg kg^-1). In addition, the co-occurrence network revealed that both macrophytes harbored two same keystone bacteria with the high betweenness centrality values, including the family Pedosphaeraceae (genus_unclassified) and genus Parasegetibacter. Their relative abundances were up to 28-fold and 25-fold higher than other keystone species, respectively. Furthermore, these two keystone bacteria were metabolic generalists with vital ecological functions, which posed significant potentials for promoting plant growth and tolerating Cd bio-toxicity. Therefore, the identified keystone rhizobacteria, Pedosphaeraceae and Parasegetibacter, would be potential microbial modulations applied for the future optimization of phytoremediation in Cd-contaminated sediment.

Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

Engineering the plant microbiota in the context of the theory of ecological communities

Crop-associated microorganisms are known to have a determining influence on crop growth and resistance to stresses. Indeed, microorganisms can deter pathogens, reduce stress levels, improve nutrition, and stimulate growth. However, the microbial communities associated with a plant are rarely optimal for agricultural needs. But how can we engineer crops-associated microbial communities? An interesting framework to address this question is the theory of ecological communities that stipulates four processes by which communities can change: 1) selection, 2) dispersal, 3) speciation and 4) ecological drift. Of these, speciation and dispersal can result in the addition of new species to the plant microbiota, whereas selection and drift can lead to the loss of species. We believe that if these mechanisms are sufficiently understood, they could be harnessed to purposefully engineer the crop microbiota. Here, we will discuss the recent efforts to modify the phenotype of plants that are aligned with these ecological processes.

Function is a better predictor of plant rhizosphere community membership than 16S phylogeny

Rhizobacterial communities are important for plant health but we still have limited understanding of how they are constructed or how they can be manipulated. High-throughput 16S rRNA sequencing provides good information on taxonomic composition but remains an unreliable proxy for phenotypes. In this study, we tested the hypothesis that experimentally observed functional traits would be better predictors of community membership than phylogenetic origin. To test this hypothesis, we sampled communities on four plant species grown in two soil types and characterized 593 bacterial isolates in terms of antibiotic susceptibility, carbon metabolism, resource use and plant growth-promoting traits. In support of our hypothesis we found that three of the four plant species had phylogenetically diverse, but functionally constrained communities. Notably, communities did not grow best on complex media mimicking their host of origin but were distinguished by variation in overall growth characteristics (copiotrophy/oligotrophy) and antibiotic susceptibility. These data, combined with variation in phylogenetic structure, suggest that different classes of traits (antagonistic competition or resource-based) are more important in different communities. This culture-based approach supports and complements the findings of a previous high-throughput 16S rRNA analysis of this experiment and provides functional insights into the patterns observed with culture-independent methods.

Insights into the taxonomic and functional characterization of agricultural crop core rhizobiomes and their potential microbial drivers

While our understanding of plant-microbe interactions in the rhizosphere microbiome (rhizobiome) has increased, there is still limited information on which taxa and functions drive these rhizobiome interactions. Focusing on the core rhizobiome (members common to two or more microbial assemblages) of crops may reduce the number of targets for determining these interactions, as they are expected to have greater influence on soil nutrient cycling and plant growth than the rest of the rhizobiome. Here, we examined whether the characterization of a core rhizobiome on the basis of only taxonomic or functional traits rather than the combined analysis of taxonomic and functional traits provides a different assessment of the core rhizobiome of agricultural crops. Sequences of the bacterial 16S rRNA gene from six globally important crops were analyzed using two different approaches in order to identify and characterize the taxonomic and functional core rhizobiome. For all crops examined, we found significant differences in the taxonomic and functional composition between the core rhizobiomes, and different phyla, genera, and predicted microbial functions were dominant depending on the core rhizobiome type. Network analysis indicated potentially important taxa were present in both taxonomic and functional core rhizobiomes. A subset of genera and predicted functions were exclusively or predominately present in only one type of core rhizobiome while others were detected in both core rhizobiomes. These results highlight the necessity of including both taxonomy and function when assessing the core rhizobiome, as this will enhance our understanding of the relationships between microbial taxa and soil health, plant growth, and agricultural sustainability.

The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA

This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security.IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.

Cadmium stress in paddy fields: Effects of soil conditions and remediation strategies

Cadmium (Cd) toxicity in paddy soil and accumulation in rice plants and grains have got global concern due to its health effects. This review highlights the effects of soil factors including soil organic matter, soil pH, redox potential, and soil microbes which influencing Cd uptake by rice plant. Therefore, a comprehensive review of innovative and environmentally friendly management practices for managing Cd stress in rice is lacking. Thus, this review discusses the effect of Cd toxicity in rice and describes management strategies to offset its effects. Moreover, future research thrusts to reduce its uptake by rice has also been highlighted. Through phytoremediation, Cd may be extracted and stabilized in the soil while through microbes Cd can be sequestrated inside the microbial bodies. Increased Cd uptake in hyperaccumulator plants to remediate and convert the toxic form of Cd into non-toxic forms. While in chemical remediation, Cd can be washed out, immobilized and stabilized in the soil through chemical amendments. The organic amendments may help through an increase in soil pH, adsorption in its functional groups, the formation of complexations, and the conversion of exchangeable to residual forms. Developing rice genotypes with restricted Cd uptake and reduced accumulation in grain through conventional and marker-assisted breeding are fundamental keys for safe rice production. In this regard, the use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics may be quite helpful.

Metagenomic Insights into Rhizospheric Microbiome Profiling in Lentil Cultivars Unveils Differential Microbial Nitrogen and Phosphorus Metabolism under Rice-Fallow Ecology

The plant rhizosphere interfaces an array of microbiomes related to plant growth and development. Cultivar-specific soil microbial communities with respect to their taxonomic structure and specific function have not been investigated explicitly in improving the adaptation of lentil cultivars under rice-fallow ecology. The present study was carried out to decipher the rhizosphere microbiome assembly of two lentil cultivars under rice-fallow ecology for discerning the diversity of microbial communities and for predicting the function of microbiome genes related to nitrogen (N) and phosphorus (P) cycling processes deploying high-throughput whole (meta) genome sequencing. The metagenome profile of two cultivars detected variable microbiome composition with discrete metabolic activity. Cyanobacteria, Bacteroidetes, Proteobacteria, Gemmatimonadetes, and Thaumarchaeota were abundant phyla in the “Farmer-2” rhizosphere, whereas Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Chloroflexi, and some incompletely described procaryotes of the “Candidatus” category were found to be robustly enriched the rhizosphere of “Moitree”. Functional prediction profiles of the microbial metagenomes between two cultivars revealed mostly house keeping genes with general metabolism. Additionally, the rhizosphere of “Moitree” had a high abundance of genes related to denitrification processes. Significant difference was observed regarding P cycling genes between the cultivars. “Moitree” with a profuse root system exhibited better N fixation and translocation ability due to a good “foraging strategy” for improving acquisition of native P under the nutrient depleted rice-fallow ecology. However, “Farmer-2” revealed a better “mining strategy” for enhancing P solubilization and further transportation to sinks. This study warrants comprehensive research for explaining the role of microbiome diversity and cultivar–microbe interactions towards stimulating microbiome-derived soil reactions regarding nutrient availability under rice-fallow ecology.

Distinct rhizobacterial functional assemblies assist two Sedum alfredii ecotypes to adopt different survival strategies under lead stress

Lead (Pb) contamination presents a widespread environmental plague. Sedum alfredii is widely used for soil phytoremediation owing to its capacity to extract heavy metals, such as Pb. Although efficient Pb extraction is mediated by complex interactions between the roots and rhizospheric bacteria, the mechanism by which S. alfredii recruits microorganisms under Pb stress remains unclear. The Pb-accumulating ecotype (AE) and non-accumulating ecotype (NAE) of S. alfredii recruited different rhizobacterial communities. Under Pb stress, AE rhizosphere-enriched bacteria assembled into stable-connected clusters with higher phylogenetic and functional diversity. These microbes, e.g., Flavobacterium, could release indoleacetic acid to promote plant growth and siderophores, thereby increasing Pb availability. The NAE rhizosphere-enriched functional bacteria "desperately" assembled into highly specialized functional clusters with extremely low phylogenetic diversity. These bacteria, e.g., Pseudomonas, could enhance phosphorus solubilization and Pb precipitation, thereby reducing Pb stress and plant Pb accumulation. High niche overlap level of the rhizo-enriched species raised challenges in soil resource utilization, whereas the NAE community assembly was markedly constrained by environmental "selection effect" than that of AE rhizobacterial community. These results indicate that different ecotypes of S. alfredii recruit distinct bacterial functional assemblies to drive specific plant-soil feedbacks for different survival in Pb-contaminated soils. To cope with heavy metal stress, NAE formed a highly functional and specialized but vulnerable community and efficiently blocked heavy metal absorption by plants. However, the AE community adopted a more stable and elegant strategy to promote plant growth and the accumulation of dry matter via multiple evolutionary strategies that ensured a high yield of heavy metal phytoextraction. This for the first time provides new insights into the roles of rhizosphere microbes in plant adaptations to abiotic stresses.

Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil

Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.

Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System

Tillage and fertilization are common practices used to enhance soil fertility and increase yield. Changes in soil edaphic properties associated with different tillage and fertility regimes have been widely examined, yet, the microbially mediated pathways and ecological niches involved in enhancing soil fertility are poorly understood. The effects of long-term conventional tillage and no-till in parallel with three fertility treatments (No fertilization, N-only, and NPK) on soil microbial communities were investigated in a long-term field study that was established in the 1970's. Here, we used high-throughput sequencing of bacterial, fungal and oomycetes markers, followed by community-level functional and ecological assembly to discern principles governing tillage and fertility practices' influence on associated soil microbiomes. Both tillage and fertilizer significantly altered microbial community structure, but the tillage effect was more prominent than the fertilizer effect. Tillage significantly affected bacteria, fungi, fusaria, and oomycete beta-diversity, whereas fertilizer only affected bacteria and fungi beta-diversity. In our study different tillage and fertilizer regimes favored specific networks of metabolic pathways and distinct ecological guilds. No-till selected for beneficial microbes that translocate nutrients and resources and protect the host against pathogens. Notably, ecological guilds featuring arbuscular mycorrhizae, mycoparasites, and nematophagous fungi were favored in no-till soils, while fungal saprotrophs and plant pathogens dominated in tilled soils. Conventional till and fertilizer management shifted the communities toward fast growing competitors. Copiotrophic bacteria and fusarium species were favored under conventional tillage and in the presence of fertilizers. The analysis of the metagenomes revealed a higher abundance of predicted pathways associated with energy metabolism, translation, metabolism of cofactors and vitamins, glycan biosynthesis and nucleotide metabolism in no-till. Furthermore, no specific pathways were found to be enriched under the investigated fertilization regimes. Understanding how tillage and fertilizer management shift microbial diversity, structure and ecological niches, such as presented here, can assist with designing farming systems that can maintain high crop yield, while reducing soil erosion and nutrient losses.

Phyllosphere bacterial assembly in citrus crop under conventional and ecological management

Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.

Metabolomic effects of the colonization of Medicago truncatula by the facultative endophyte Arthrobacter agilis UMCV2 in a foliar inoculation system

Biofertilizer production and application for sustainable agriculture is already a reality. The methods for biofertilizers delivery in crop fields are diverse. Although foliar spray is gaining wide acceptance, little is known about the influence that the biochemical features of leaves have on the microbial colonization. Arthrobacter agilis UMCV2 is a rhizospheric and endophytic bacteria that promotes plant growth and health. In this study, we determined the capacity of the UMCV2 strain to colonize different leaves from Medicago truncatula in a foliar inoculation system. By using two powerful analytical methods based on mass spectrometry, we determined the chemical profile of the leaves in 15-d old plants. The metabolic signatures between the unifoliate leaf (m1) and the metameric units developing above (m2 and m3) were different, and interestingly, the highest colony forming units (CFU) was found in m1. The occurrence of the endophyte strongly affects the sugar composition in m1 and m2 leaves. Our results suggest that A. agilis UMCV2 colonize the leaves under a foliar inoculation system independently of the phenological age of the leaf and it is capable of modulating the carbohydrate metabolism without affecting the rest of the metabolome.

Mechanisms of water regime effects on uptake of cadmium and nitrate by two ecotypes of water spinach (Ipomoea aquatica Forsk.) in contaminated soil

Availability of cadmium (Cd) and nitrate and their transfer to green leafy vegetables is highly dependent on physical, chemical and biochemical conditions of the soil. The phenotypic characteristics, accumulation of hazardous materials and rhizosphere properties of two ecotypes of water spinach in response to water stress were investigated. Flooding significantly enhanced plant growth and decreased Cd and nitrate concentrations in the shoot and root of both ecotypes of water spinach. Flooding extensively changed the physicochemical properties and biological processes in the rhizosphere, including increased pH and activities of urease and acid phosphatase, and decreased availability of Cd and nitrate and activity of nitrate reductase. Furthermore, flooding increased rhizosphere bacteria community diversity (including richness and evenness) and changed their community structure. Denitrifying bacteria (Clostridiales, Azoarcus and Pseudomonas), toxic metal resistant microorganisms (Rhodosporillaceae, Rhizobiales and Geobacter) were enriched in the rhizosphere under flooding conditions, and the plant growth-promoting taxa (Sphingomonadaceae) were preferentially colonized in the high accumulator (HA) rhizosphere region. These results indicated that flooding treatments result in biochemical and microbiological changes in soil, especially in the rhizosphere and reduced the availability of Cd and nitrate to plants, thus decreasing their uptake by water spinach. It is, therefore, possible to promote crop growth and reduce the accumulation of hazardous materials in vegetable crops like water spinach by controlling soil moisture conditions.

Wheat dwarfing influences selection of the rhizosphere microbiome

The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.

Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil

Pseudomonas putida is one of 13 major groups of Pseudomonas spp. and contains numerous species occupying diverse niches and performing many functions such as plant growth promotion and bioremediation. Here we compared a set of 19 P. putida isolates obtained from sugarcane rhizosphere or bulk soil using a population genomics approach aiming to assess genomic and metabolic differences between populations from these habitats. Phylogenomics placed rhizosphere versus bulk soil strains in separate clades clustering with different type strains of the P. putida group. Multivariate analyses indicated that the rhizosphere and bulk soil isolates form distinct populations. Comparative genomics identified several genetic functions (GO-terms) significantly different between populations, including some exclusively present in the rhizosphere or bulk soil strains, such as D-galactonic acid catabolism and cellulose biosynthesis, respectively. The metabolic profiles of rhizosphere and bulk soil populations analyzed by Biolog Ecoplates also differ significantly, most notably by the higher oxidation of D-galactonic/D-galacturonic acid by the rhizosphere population. Accordingly, D-galactonate catabolism operon (dgo) was present in all rhizosphere isolates and absent in the bulk soil population. This study showed that sugarcane rhizosphere and bulk soil harbor different populations of P. putida and identified genes and functions potentially associated with their soil niches.

Rhizosphere response to nickel in a facultative hyperaccumulator

This study faces the characterization of the culturable microbiota of the facultative Ni-hyperaccumulator Alyssoides utriculata to obtain a collection of bacterial and fungal strains for potential applications in Ni phytoextraction. Rhizosphere soil samples and adjacent bare soil associated with A. utriculata from serpentine and non-serpentine sites were collected together with plant roots and shoots. Rhizobacteria and fungi were isolated and characterized genotypically and phenotypically. Plants and soils were analyzed for total element concentration using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Serpentine and non-serpentine sites differ in terms of elements concentration in soil, plant roots and shoots. Ni and Co are significantly higher on serpentine site, while Ca is more abundant in non-serpentine site. Bacteria and fungi were significantly more abundant in rhizosphere than in bare soil and were dominated by genera Arthrobacter, Bacillus and Streptomyces, Penicillium and Mucor. The genus Pseudomonas was only found in rhizospheric serpentine soils (<2% of total serpentine isolates) and with Streptomyces sp. showed highest Ni-tolerance up to 15 mM. The same occurred for Trichoderma strain, belonging to the harzianum group (<2% of the total microfungal count) and Penicillium ochrochloron (<10% of the total microfungal count, tolerance up to Ni 20 mM). Among serpentine bacterial isolates, 8 strains belonging to 5 genera showed at least one PGPR activity (1-Aminocyclopropane-1-Carboxylic Acid (ACC) deaminase activity, production of indole-3-acetic acid (IAA), siderophores and phosphate solubilizing capacity), especially genera Pantoea, Pseudomonas and Streptomyces. Those microorganisms might thus be promising candidates for employment in bioaugmentation trials.

Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems

Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.

Community diversity and potential functions of rhizosphere-associated bacteria of nickel hyperaccumulators found in Albania

Ultramafic (i.e. serpentine) soils are widespread in the Balkans and particularly in Albania. They account for a large part of plant endemism in that region and host several hyperaccumulator species, which are characterized by leaf nickel concentrations frequently above 1%. This rich nickel hyperaccumulating flora could serve as candidate to be used in phytoextraction and agromining. Despite recent interest in metal hyperaccumulating plants and agromining, very few studies have investigated the bacterial diversity and the influence of environmental factors on microbial gene profiles in the rhizosphere of hyperaccumulator plants growing on ultramafic soils. Because rhizospheric bacteria could be crucial to the success of phytoremediation, we studied a total of 48 nickel-hyperaccumulating plants which were sampled from four species that are widespread in Albania: Noccaea ochroleuca, Odontarrhena smolikana, O. rigida and O. chalcidica. All samples were taken from the ultramafic regions of Librazhd and Pogradec in eastern Albania in October 2015. Our study shows that Proteobacteria, Actinobacteria and Acidobacteria dominated the soil bacterial communities. Of these three phyla, only Proteobacteria was relatively abundant. This study underlines the influence of soil Cation Exchange Capacity on the bacterial community's diversity and structure. Based on the predicted metagenomes, the genes belonging to amino acid, lipid and carbohydrate metabolisms were identified as major gene families. Our study sheds some light on our understanding of how bacterial communities are structured within and affect the rhizosphere of hyperaccumulator plants from ultramafic soils in Albania.

Comparison of rhizosphere bacterial communities of reed and Suaeda in Shuangtaizi River Estuary, Northeast China

Microbial communities in wetland soils play vital roles in biogeochemical cycling of nutrients. In this study, the soil samples were collected from Suaeda, reed and Suaeda-reed hybrid zones in Shuangtaizi River Estuary, Northeast China, and the rhizosphere bacterial communities were compared using Illumina MiSeq sequencing. The microbial richness, diversity and structure of bacterial communities varied greatly in reed and Suaeda. Canonical correspondence analysis and Mantel test indicated that pH was the most significant factor (P < 0.05) in bacterial community assembly. Proteobacteria was the most dominant phylum, accounting for 45.7-58.0% of the total sequences. Thioprofundum, Thiohalomonas and Exiguobacterium were the predominant genera in Suaeda, while Exiguobacterium, Gillisia, Desulfomonile, Citrobacter, Thioprofundum and Acinetobacter were the core species in reed. PICRUSt analysis revealed similar functional profiles of rhizosphere microbiota in reed and Suaeda. Nitrate reduction related genes were abundant for nitrogen metabolism, whereas assimilatory sulfate reduction was the major process for sulfur metabolism.

Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere Communities

The rhizosphere encompasses the soil surrounding the surface of plants’ fine roots. Accordingly, the microbiome present is influenced by both soil type and plant species. Furthermore, soil microbial communities respond to land-use intensity due to the effects on soil conditions and plant performance. However, there is limited knowledge about the impact of grassland management practices under field conditions on the composition of both bacteria and fungi in the rhizosphere of different plant functional groups. In spring 2014 we planted four phytometer species, two forbs (Plantago lanceolata, Achillea millefolium) and two grasses (Dactylis glomerata, Arrhenatherum elatius) into 13 permanent experimental grassland plots, differing in management. After 6 months, rhizosphere and bulk soil associated with the phytometer plants were sampled, microbial genomic DNA was extracted and bacterial 16S and fungal ITS rDNA were sequenced using Illumina MiSeq. Our study revealed that the rhizosphere microbial community was more diverse than the bulk soil community. There were no differences in microbial community composition between the two plant functional groups, but a clear impact of root traits and edaphic conditions. Land-use intensity strongly affected plant productivity, neighboring plant richness and edaphic conditions, especially soil C/N ratio, which in turn had a strong influence on root traits and thereby explained to large extent microbial community composition. Rhizosphere microbes were mainly affected by abiotic factors, in particular by land-use intensity, while plant functional type had only subordinate effects. Our study provides novel insights into the assembly of rhizosphere bacterial and fungal communities in response to land-use intensity and plant functional groups in managed grassland ecosystems.

Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L.)

Cadmium accumulation in rice grains is highly dependent on its bioavailability that affected by various physicochemical properties and microbiological processes of soil. The rhizospheric bacterial communities of rice grown in contaminated soils by means of rice cultivars highly or weakly accumulating Cd in grains (HA and LA, respectively) were investigated. HA roots absorbed 7.26- and 2.25-fold more Cd than did LA roots at low (0.44 mg kg^-1) and high (6.66 mg kg^-1) soil Cd levels, respectively. Regardless of Cd levels, Cd bioavailability in the rhizosphere of HA was significantly higher than that of LA. Planting of rice and elevated Cd levels both significantly decreased bacterial α-diversity and altered bacterial community structure, with noticeable differences between the rice cultivars. Taxa specifically enriched in the HA rhizosphere (phyla Bacteroidetes, Firmicutes, and Deltaproteobacteria) can directly or indirectly participate in metal activation, whereas the LA rhizosphere was highly colonized by plant growth-promoting taxa (phyla Alphaproteobacteria and Gammaproteobacteria). The results indicate a potential association of Cd uptake and accumulation with rhizosphere bacteria in rice grown on a contaminated soil, thus providing baseline data and a new perspective on the maintenance of rice security.

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population

Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.

Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay

Harmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes. Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae were the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyll a contents, which were affected mainly by Skeletonema costatum Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCE Harmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.

Cadmium Exposure-Sedum alfredii Planting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

Rhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE) Sedum alfredii in comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes of S. alfredii and elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa from Actinobacteria, Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genus Streptomyces was responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance of Streptomyces was 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulator S. alfredii and Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genus Streptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfredii is a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulator S. alfredii Here, we report the investigation of rhizosphere bacterial communities of S. alfredii in phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genus Streptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

Endophytic bacteria are nearly ubiquitously present in the internal tissues of plants, and some endophytes can promote plant growth. In this study, we sampled the roots of four ancestral species of sugarcane (two genotypes per species) and two sugarcane cultivars, and used 16S rRNA and nifH gene sequencing to characterize the root endophytic bacterial communities and diazotroph diversity. A total of 7,198 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. The endophytic bacterial communities exhibited significantly different α- and β-diversities. From the 202 detected families in the sugarcane roots, a core microbiome containing 13 families was identified. The nifH gene was successfully detected in 9 of 30 samples from the four sugarcane species assayed, and 1,734 OTUs were merged for endophytic diazotrophs. In the tested samples, 43 families of endophytic diazotrophs were detected, and six families showed differences across samples. Among the 20 most abundant detected genera, 10 have been reported to be involved in nitrogen fixation in sugarcane. These findings demonstrate the diversity of the microbial communities in different sugarcane germplasms and shed light on the mechanism of biological nitrogen fixation in sugarcane.

Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity

Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P. jessenii subgroup. The remaining 18 isolates fell into two phylogenetic subclades distinct from currently recognized P. fluorescens subgroups, and probably represent new subgroups. Consistent with their phylogenetic distance from described subgroups, the genome sequences of strains in these subclades are asyntenous to the genome sequences of members of their neighbour subgroups. The tropical isolates have several functional genes also present in known fluorescent Pseudomonas spp. strains. However, members of the new subclades share exclusive genes not detected in other subgroups, pointing to the potential for novel functions. Additionally, we identified 12 potential new species among the 76 isolates from the tropical soil. The unexplored diversity found in the tropical soil is possibly related to biogeographical patterns.

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica

In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.

Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.

Let the Core Microbiota Be Functional

The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.