Fungal and bacterial communities in the rhizosphere of Pinus tabulaeformis related to the restoration of plantations and natural secondary forests in the Loess Plateau, northwest China

An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG

AIMS

The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs).

METHODS AND RESULTS

The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible.

CONCLUSION

NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.

Streptomyces solincola sp. nov., isolated from soil in Malaysia

A urease-producing Gram-stain-positive actinobacterium, designated strain T5^T, was isolated from a soil sample collected at a highway hillslope in Selangor, Malaysia. The strain was found to produce pale yellowish-pink aerial mycelia with smooth long chain spores and extensively branched light yellowish-pink substrate mycelia on oatmeal agar. Strain T5^T grew at 15-37 °C, pH 6-11, and tolerated up to 9 % (w/v) NaCl, with optimal growth occurring at 28 °C, pH 6-9 and without NaCl. The whole-cell sugar hydrolysate of strain T5^T contained galactose, glucose and ribose. The ll-diaminopimelic acid isomer was detected in the cell wall. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol were found to be the predominant polar lipids. The main fatty acids were anteiso-C_17 : 0, iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_14 : 0. Comparative analysis of the 16S rRNA gene sequences indicated that strain T5^T belonged to Streptomyces of the family Streptomycetaceae with the highest 16S rRNA gene sequence similarity to Streptomyces lichenis LCR6-01^T (99.0 %). The overall genome relatedness indices revealed that the closest related species was S. lichenis LCR6-01^T with 89.4 % average nucleotide identity and 33.7 % digital DNA-DNA hybridization. Phylogeny analyses showed that strain T5^T was closely related to Streptomyces fradiae, Streptomyces lavendofoliae, Streptomyces lichenis, Streptomyces roseolilacinus and Streptomyces somaliensis. Based on these polyphasic data, strain T5^T represents a novel species, for which the name Streptomyces solincola sp. nov. is proposed. The type strain is T5^T (=TBRC 5137^T= DSM 42166^T).

Chemodiversity of Soil Dissolved Organic Matter and Its Association With Soil Microbial Communities Along a Chronosequence of Chinese Fir Monoculture Plantations

The total dissolved organic matter (DOM) content of soil changes after vegetation transformation, but the diversity of the underlying chemical composition has not been explored in detail. Characterizing the molecular diversity of DOM and its fate enables a better understanding of the soil quality of monoculture forest plantations. This study characterized the chemodiversity of soil DOM, assessed the variation of the soil microbial community composition, and identified specific linkages between DOM molecules and microbial community composition in soil samples from a 100-year chronosequence of Chinese fir monoculture plantations. With increasing plantation age, soil total carbon and dissolved organic carbon first decreased and then increased, while soil nutrients, such as available potassium and phosphorus and total nitrogen, potassium, and phosphorus, increased significantly. Lignin/carboxylic-rich alicyclic molecule (CRAM)-like structures accounted for the largest proportion of DOM, while aliphatic/proteins and carbohydrates showed a decreasing trend along the chronosequence. DOM high in H/C (such as lipids and aliphatic/proteins) degraded preferentially, while low-H/C DOM (such as lignin/CRAM-like structures and tannins) showed recalcitrance during stand development. Soil bacterial richness and diversity increased significantly as stand age increased, while soil fungal diversity tended to increase during early stand development and then decrease. The soil microbial community had a complex connectivity and strong interaction with DOM during stand development. Most bacterial phyla, such as Acidobacteria, Chloroflexi, and Firmicutes, were very significantly and positively correlated with DOM molecules. However, Verrucomicrobia and almost all fungi, such as Basidiomycota and Ascomycota, were significantly negatively correlated with DOM molecules. Overall, the community of soil microorganisms interacted closely with the compositional variability of DOM in the monoculture plantations investigated, both by producing and consuming DOM. This suggests that DOM is not intrinsically recalcitrant but instead persists in soils as a result of simultaneous consumption, transformation, and formation by soil microorganisms with extended stand ages of Chinese fir plantations.

Inoculation With Ectomycorrhizal Fungi and Dark Septate Endophytes Contributes to the Resistance of Pinus spp. to Pine Wilt Disease

Pine wilt disease (PWD) is a deadly disease to pines (Pinus spp.) worldwide. The occurrence of PWD can reduce the relative abundance of root ectomycorrhizal fungi (ECMF) and dark septate endophytes (DSE). However, the effects of exogenous ECMF/DSE inoculation on the rhizosphere microbial community structure of Pinus tabulaeformis infected by pine wood nematode (PWN) is little known. Here, we tested how ECMF/DSE may improve resistance to PWD by quantifying microbial carbon biomass and soil enzymatic activity among different treatments at 6 and 9 months after PWN infection. Denaturing gradient gel electrophoresis (DGGE) was used to study the microbial community structure at 3, 6, and 9 months after PWN infection in the rhizosphere of P. tabulaeformis seedlings inoculated with ECMF/DSE. The results showed that exogenous ECMF/DSE inoculation reduced the disease severity caused by PWN infection. After PWN infection, the rhizosphere microbial carbon of seedlings inoculated with Amanita vaginata, Suillus bovinus, Gaeumannomyces cylindrosporus, and Paraphoma chrysanthemicola was 38.16, 49.67, 42.11, and 96.05% higher than that of the control group, respectively. Inoculation of ECMF/DSE inhibited the decrease of rhizosphere microbial biomass caused by PWN infection. The richness and diversity of P. tabulaeformis rhizosphere fungi at 9 months were reduced by PWN infection but partially recovered by the exogenous fungi (ECMF/DSE) inoculation except for P. chrysanthemicola, which indicates a role of ECMF/DSE in maintaining stability of the microbial community. Inoculation with ECMF/DSE increased the beneficial bacterial (Thauera sp., Mesorhizobium sp., etc.) and fungal groups (Tomentella ellisii, Wilcoxina mikolae, etc.) of in the rhizosphere. In summary, exogenous ECMF/DSE inoculation could increase P. tabulaeformis resistance to PWD probably by improving the rhizosphere microenvironment.

Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery

Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka-Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.

Community structure and diversity of the microbiomes of two microhabitats at the root-soil interface: implications of meta-analysis of the root-zone soil and root endosphere microbial communities in Xiong'an New Area

The diversity of the microbial compositions of the root-zone soil (the rhizosphere-surrounding soil) and root endosphere (all inner root tissues) of Pinus tabulaeformis Carr. and Ginkgo biloba L. were evaluated in Xiong'an New Area using high-throughput sequencing; the influence of the soil edaphic parameters on microbial community compositions was also evaluated. Our results showed that both the taxonomic and phylogenetic diversities of the root endosphere were lower than those of the root-zone soil, but the variation in the endosphere microbial community structure was remarkably higher than that of the root-zone soil. Spearman correlation analysis showed that the soil organic matter, total nitrogen, total phosphate, total potassium, ratio of carbon to nitrogen, and pH significantly explained the α-diversity of the bacterial community and that total nitrogen differentially contributed to the α-diversity of the fungal community. Variation partitioning analysis showed that plant species had a greater influence on microbial composition variations than did any other soil property, although soil chemical parameters explained more variation when integrated. Together, our results suggest that both plant species and soil chemical parameters played a critical role in shaping the microbial community composition.

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China

The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities.

Root-Associated Microbial Communities of Abies nordmanniana: Insights Into Interactions of Microbial Communities With Antioxidative Enzymes and Plant Growth

Abies nordmanniana is a major Christmas tree species in Europe, but their uneven and prolonged growth slows down their production. By a 16S and 18S rRNA gene amplicon sequencing approach, we performed a characterization of root-associated bacterial and fungal communities for three-year-old A. nordmanniana plants collected from two nurseries in Denmark and Germany and displaying different growth patterns (small versus tall plants). Proteobacteria had the highest relative abundance at both sampling sites and plant sizes, and Ascomycota was the most abundant fungal phylum. At the order level, Acidobacteriales, Actinomycetales, Burkholderiales, Rhizobiales, and Xanthomonadales represented the bacterial core microbiome of A. nordmanniana, independently of the sampling site or plant size, while the fungal core microbiome included members of the Agaricales, Hypocreales, and Pezizales. Principal Coordinate Analysis indicated that both bacterial and fungal communities clustered according to the sampling site pointing to the significance of soil characteristics and climatic conditions for the composition of root-associated microbial communities. Major differences between communities from tall and small plants were a dominance of the potential pathogen Fusarium (Hypocreales) in the small plants from Germany, while Agaricales, that includes reported beneficial ectomycorrhizal fungi, dominated in the tall plants. An evaluation of plant root antioxidative enzyme profiles showed higher levels of the antioxidative enzymes ascorbate peroxidase, peroxidase, and superoxide dismutase in small plants compared to tall plants. We suggest that the higher antioxidative enzyme activities combined with the growth arrest phenotype indicate higher oxidative stress levels in the small plants. Additionally, the correlations between the relative abundances of specific taxa of the microbiome with the plant antioxidative enzyme profiles were established. The main result was that many more bacterial taxa correlated positively than negatively with one or more antioxidative enzyme activity. This may suggest that the ability of bacteria to increase plant antioxidative enzyme defenses is widespread.

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau.

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.

Comparative Metagenomics Reveal Phylum Level Temporal and Spatial Changes in Mycobiome of Belowground Parts of Crocus sativus

Plant-fungal associations have been explored by routine cultivation based approaches and cultivation based approaches cannot catalogue more than 5% of fungal diversity associated with any niche. In the present study, an attempt has been made to catalogue fungal diversity associated with belowground parts i.e. rhizosphere and cormosphere, of Crocus sativus (an economically important herb) during two growth stages, using cultivation independent ITS gene targeted approach, taking bulk soil as reference. The 454 pyrosequencing sequence data analysis suggests that the fungal diversity was niche and growth stage specific. Fungi diversity, in the present case, was not only different between the two organs (roots and corm) but the dominance pattern varies between the cormosphere during two growth stages. Zygomycota was dominant fungal phylum in the rhizosphere whereas Basidiomycota was dominant in cormosphere during flowering stage. However in cormosphere though Basidiomycota was dominant phylum during flowering stage but Zygomycota was dominant during dormant stage. Interestingly, in cormosphere, the phyla which was dominant at dormant stage was rare at flowering stage and vice-versa (Basidiomycota: Flowering = 93.2% Dormant = 0.05% and Zygomycota: Flowering = 0.8% Dormant = 99.7%). At genus level, Rhizopus was dominant in dormant stage but was rare in flowering stage (Rhizopus: Dormant = 99.7% Flowering = 0.55%). This dynamics is not followed by the bulk soil fungi which was dominated by Ascomycota during both stages under study. The genus Fusarium, whose species F. oxysporum causes corm rot in C. sativus, was present during both stages with slightly higher abundance in roots. Interestingly, the abundance of Rhizopus varied a great deal in two stages in cormosphere but the abundance of Fusarium was comparable in two growth stages (Bulk soil Flowering = 0.05%, Rhizosphere Flowering = 1.4%, Cormosphere Flowering = 0.06%, Bulk soil Dormant = 2.47% and cormosphere dormant = 0.05%). This is the first report on the fungal diversity associated with the root of Crocus sativus and first report on the fungi associated with corm of any plant with the temporal and spatial variation in the fungal community structure.

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

Investigation and analysis of microbiological communities in natural Ophiocordyceps sinensis

Ophiocordyceps sinensis is a fungus that parasitizes caterpillars, and more than 30 species of filamentous fungi have been isolated from its fruiting body. However, its microbiological diversity remains unclear. Based on the clone library and quantitative PCR techniques, the bacterial flora and mycobiota of 3 different samples (larva, stromata/sclerotia, and surface soil) from natural O. sinensis specimens were investigated using primer sets that targeted the 16S rRNA gene and internal transcribed spacer region of ribosomal DNA. The results showed that the abundance of bacterial and fungal communities in the soil attached to the surface of O. sinensis was (6.4 ± 1.4) × 10(6) and (6.0 ± 0.3) × 10(7) copies/g dry matter, respectively, which was the highest compared with that in the larva and stromal samples. The main groups of bacteria in the O. sinensis samples were Proteobacteria and Actinobacteria, while Ascomycota was the most dominant fungal group in the 3 samples. At the genus level, Geomyces, Phoma, and Trichocladium were the dominant genera in the larval sample, while Geomyces and Cladosporium were the dominant genera in the stromal sample. In conclusion, a great number of bacterial and fungal species were present in naturally occurring O. sinensis specimens, and there was a high diversity of bacterial and fungal communities. These findings contribute to the understanding of the bacterial and fungal community structure of this valuable medicinal fungus and lay the foundation for the future discovery of new medicinal microorganism resources.