Phyla In Soils Research Articles

Synergistic regulation of salinity and nutrients on organic carbon mineralization in a 700-year cultivated saline soil chronosequence

Long-term cultivation in reclaimed mudflats significantly impacts soil properties through changes in salinity and organic carbon (OC) inputs, which subsequently affect soil physical, chemical, and biological characteristics. In addition, long-term rice cultivation can help optimize soil health and fertility management in paddy fields, mitigate climate change, and enhance ecosystem services. However, the impact of long-term cultivation on OC mineralization across a salinity gradient remains unclear. During an 80-d incubation experiment, we assessed 13C-labeled glucose mineralization in soils cultivated for 5, 20, 200, and 700 years, each with varying salinity levels. Our results demonstrated that glucose mineralization declined linearly with increasing soil salinity, from 76 % in low-salinity soils to 31 % in high-salinity soils, reflecting a clear physical impact. This process was closely linked with chemical properties, showing a positive correlation with Olsen P and levels of microbial biomass carbon and nitrogen. Soil organic carbon (SOC) mineralization was primarily controlled by dissolved OC regardless of soil salinity. Further investigation revealed significant shifts in the biological properties, notably the bacterial community composition, which varied with the duration of soil cultivation. The bacterial Shannon index increased steadily from 50 to 700 years, forming distinct clusters, influenced primarily by electrical conductivity and pH in high-salinity soils and by soil-labile nutrients in low-salinity soils. The abundance of Acidobacteria, Proteobacteria, and Verrucomicrobia—dominant phyla in soil cultivated for 700 years—is negatively correlated with soil salinity and pH and positively with labile nutrients, glucose, and OC mineralization, whereas the opposite was true for Bacteroidetes and Firmicutes dominant phyla in soil cultivated for 5 years, was affected positively by soil salinity and pH and negatively by labile nutrients and glucose mineralization. In conclusion, soil salinity and nutrients synergistically regulate OC mineralization in a 700-year cultivated saline soil chronosequence. Addressing these factors is critical to enhancing microbial activity and OC accumulation in saline soils, underscoring the importance of integrating measures to reduce salt and increase the import and accumulation of exogenous organic matter.

The source and dissemination of ARGs in pristine environments: Elucidating the role of migratory birds in the Arctic

Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.

Stabilization of Cd-contaminated Soil with Thiol-modified Biochar and Response of Soil Microorganisms

To explore the stabilization effect of livestock manure biochar on Cd-contaminated soil and its impact on the soil environment, a pot experiment was conducted to investigate the stabilization efficiency of cattle manure-biochar （BC） and thiol-modified biochar （SBC） on Cd in soil and their effect on the soil properties and microbial community. The structural equation model （SEM） was used to analyze the effect pathways of BC and SBC on the soil microbial community. The results showed that BC and SBC increased soil pH, available potassium, available phosphorus, and organic matter content but decreased soil available nitrogen content compared with those in CK. The stabilization efficiency of BC for Cd in soil was 14.97%, which was much lower than that of SBC （85.71%）. Moreover, SBC increased the abundance of dominant bacterial phyla in soil, with Proteobacteria, Bacteroidota, and Cyanobacteria increasing most significantly. SBC decreased the diversity of soil microorganisms, but the decrease was insignificant （P≥0.05） compared with that in CK and BC. SEM analysis indicated that the available phosphorus, available potassium, organic matter, and soil pH were the key factors influencing Cd availability in soil, whereas organic matter and Cd availability were the key factors affecting the soil microbial community. Overall, SBC could stabilize Cd effectively and increase the abundance of dominant bacteria and has great potential in the remediation of Cd-contaminated soil.

Soil mycobiome and forest endophytic fungi: Is there a relationship between them?

Fungi are important ecological agents in forests that contribute to increase the resilience of the whole ecosystem against environmental challenges. Mediterranean forests rank among the habitats most threatened by climate change and the spread of pests and diseases, which ultimately lead them into a spiral of decline. As such, changes in the composition of soil and trees’ mycobiota might correlate with health status of the forest and has been scarcely addressed in Mediterranean tree species. In this work, rhizosphere and bark-wood samples from declining Spanish forests of Castanea sativa Mill. (chestnut), Quercus ilex L. (holm oak), Q. suber L. (cork oak) and Q. pyrenaica Willd. (Pyrenean oak) were compared. Fungal communities were characterised by means of ITS metabarcoding. Higher diversity in terms of richness was found in soil, with 674 genera belonging to 15 phyla in soil vs 420 genera and 6 phyla in trees. Fungal genera exclusive to declining forests’ soils and trees didn’t include pathogenic organisms, thus preventing the association of certain genera with forest decline. Alpha diversity didn’t correlate with health status or sample type either, as it only increased in soils of asymptomatic chestnuts and not in any of the other analysed tree species. Some differentially abundant genera found in asymptomatic trees, such as Metarhizium, Aspergillus, Russula, Chaetomium, Mortierella or Cladophialophora, may be related to the biological control of decline-contributing pathogens. Finally, no relationship was found between health status and the primary lifestyles of fungi in soil and bark, which can be interpreted as a sign of resilience against adversities following cross-talk between soil and plant fungal communities.

Illumina 16S rRNA Gene Sequencing Dataset of Bacterial Communities of Soil Associated with Ironwood Trees (Casuarina equisetifolia) in Guam

Ironwood trees, which are of great importance for the economy and environment of tropical areas, were first discovered to suffer from a slow progressive dieback in Guam in 2002, later referred to as ironwood tree decline (IWTD). A variety of biotic factors have been shown to be associated with IWTD, including putative bacterial pathogens Ralstonia solanacearum and Klebsiella species (K. variicola and K. oxytoca), the fungus Ganoderma australe, and termites. Due to the soilborne nature of these pathogens, soil microbiomes have been suggested to be a significant factor influencing tree health. In this project, we sequenced the microbiome in the soil collected from the root region of healthy ironwood trees and those showing signs of IWTD to evaluate the association between the bacterial community in soil and IWTD. This dataset contains 4,782,728 raw sequencing reads present in soil samples collected from thirty-nine ironwood trees with varying scales of decline severity in Guam obtained via sequencing the V1–V3 region of the 16S rRNA gene on the Illumina NovaSeq (2 × 250 bp) platform. Sequences were taxonomically assigned in QIIME2 using the SILVA 132 database. Firmicutes and Actinobacteria were the most dominant phyla in soil. Differences in soil microbiomes were detected between limestone and sand soil parent materials. No putative plant pathogens of the genera Ralstonia or Klebsiella were found in the samples. Bacterial diversity was not linked to parameters of IWTD. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA883256. This dataset can be used to compare the bacterial taxa present in soil associated with ironwood trees in Guam to bacteria communities of other geographical locations to identify microbial signatures of IWTD. In addition, this dataset can also be used to investigate the relationship between soil microbiomes and the microbiomes of ironwood trees as well as those of the termites which attack ironwood trees.

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.

The Effects of Oil and Gas Produced Water on Soil Bacterial Community Structure in the Arid Desert Area.

The safe utilization and risk assessment of produced water (PW) from oil and gas fields for desert irrigation have received increasing attention in recent years. In this context, this study aimed to analyze structural changes in soil bacterial community, and assess the environmental impact of PW discharge and irrigation over time. High-throughput sequencing technology was employed to examine the structure of the soil bacterial community in the constructed wetland and its surrounding desert vegetation irrigation region where PW was released for a considerable amount of time (30 years). The results revealed that long-term discharge of PW and irrigation significantly reduced the abundance of the soil bacterial community but did not significantly alter the richness and diversity of the soil bacterial community. Proteobacteria was the dominant bacterial phyla in soil, but in irrigated and drained areas, the dominant bacterial phyla changed from Alphaproteobacteria to Gammaproteobacteria, the Firmicutes abundance was significantly reduced.

Molecular insights into effects of PBAT microplastics on latosol microbial diversity and DOM chemodiversity

The impact of biodegradable microplastics on the microbial community and dissolved organic matter (DOM) in latosol has not been well reported. In this study, an incubation experiment at 25 ºC for 120 days using latosol amended with low (5%) and high (10%) concentrations of polybutylene adipate terephthalate (PBAT) microplastics was carried out to explore the impacts of PBAT microplastics on soil microbial communities and DOM chemodiversity, and the intrinsic interactions between their shifts. The main bacterial and fungal phyla in soil, namely Chloroflexi, Actinobacteria, Chytridiomycota, and Rozellomycota showed a nonlinear relationship with PBAT concentration and played a pivotal role in shaping DOM chemodiversity. A higher decreased levels of lignin-like compounds and increased levels of protein-like and condensed aromatic compounds in the 5% treatment were observed than that in the 10% treatment. Furthermore, a higher increase relative abundance of CHO compounds in the 5% treatment than in the 10% treatment was ascribed to its higher oxidation degree. Co-occurrence network analysis suggested that bacteria formed more complex relationships with DOM molecules than fungi did, indicating their critical roles in DOM transformation. Our study has important implications for understanding the potential influence of biodegradable microplastics on carbon biogeochemical roles in soil.

Effects of Green Manures on Rhizosphere Fungal Community Composition of Cucumber Seedlings

Green manures are usually used to improve soil health and increase crop productivity. The activity and composition of the soil microbial community could be altered by green manures. High-throughput amplicon sequencing was used to assess the effects of green manures of wheat (Triticum aestivum) and Indian mustard (Brassica juncea) on the rhizosphere fungal community composition of cucumber (Cucumis sativus L). Results showed that green manures of wheat and Indian mustard altered the composition but not the diversity of rhizosphere fungal communities of cucumber Contents of inorganic N, Olsen P, and available K in bulk soil decreased by green manure treatments. Ascomycota, Zygomycota, and Basidiomycota were the predominant phyla in soil, and their relative abundance changed after treatment with wheat and Indian mustard. The relative abundance of Basidiomycota was increased in the green manure of wheat, while that of Zygomycota was decreased in the green manure of Indian mustard. The relative abundance of Ascomycota increased in both wheat and Indian mustard. Green manures of wheat and Indian mustard also increased the relative abundances of unclassified Sordariomycetes and Fusarium spp., whereas they decreased the relative abundances of Pseudallescheria, Mortierella, Kernia, and unclassified Chaetomiaceae spp. Compared with other treatments, green manures of wheat increased the relative abundance of Waitea sp. and decreased the relative abundance of Cephaliophora sp. Indian mustard increased the relative abundance of Humicola sp.

Variation of soil bacterial communities in a chronosequence of citrus orchard

PurposeSoil microorganisms are vital for soil ecosystems through bioconversion of soil nutrients and maintenance of soil fertility to promoting the growth and development of citrus. However, understanding of how different planting years affect the soil bacterial community structures as related to nutrient availability in citrus orchards is limited.MethodsHere, Illumina MiSeq technology was used to investigate changes in bacterial community structures with different ages of citrus orchards that were 2, 5, 10, 15, and 18 years old.ResultsThe data showed that (1) soil bacterial community structures changed over the different growth stages of citrus orchards. With the extension of plantation age, the microbial diversity of citrus orchards increased gradually so that it was highest in 10-year-old citrus plantations but then decreased where the diversity of 18-year-old citrus ages was significantly lower than that of 10 and 15-year-old ones. Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were the four dominant phyla in soil of citrus orchards, accounting for 30.85%, 24.89%, 14.27%, and 14.05% of the total soil bacterial communities, respectively. (2) Soil bacterial community structures in different succession stages were affected by soil pH and nutrients, in particular available potassium (AK).ConclusionThis study advances the understanding of soil microbiota of orchards and their interactions related to environmental factors in citrus orchard, which will improve our ability to promote the function of soil bacteria, so as to improve soil pH and reduce potassium (K) fertilizer input and improve the fruit quality.

Bacterial Communities of Forest Soils along Different Elevations: Diversity, Structure, and Functional Composition with Potential Impacts on CO2 Emission.

Soil bacteria are important components of forest ecosystems, there compostion structure and functions are sensitive to environmental conditions along elevation gradients. Using 16S rRNA gene amplicon sequencing followed by FAPROTAX function prediction, we examined the diversity, composition, and functional potentials of soil bacterial communities at three sites at elevations of 1400 m, 1600 m, and 2200 m in a temperate forest. We showed that microbial taxonomic composition did not change with elevation (p = 0.311), though soil bacterial α-diversities did. Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia were abundant phyla in almost all soil samples, while Nitrospirae, closely associated with soil nitrogen cycling, was the fourth most abundant phylum in soils at 2200 m. Chemoheterotrophy and aerobic chemoheterotrophy were the two most abundant functions performed in soils at 1400 m and 1600 m, while nitrification (25.59% on average) and aerobic nitrite oxidation (19.38% on average) were higher in soils at 2200 m. Soil CO2 effluxes decreased (p < 0.050) with increasing elevation, while they were positively correlated (r = 0.55, p = 0.035) with the abundances of bacterial functional groups associated with carbon degradation. Moreover, bacterial functional composition, rather than taxonomic composition, was significantly associated with soil CO2 effluxes, suggesting a decoupling of taxonomy and function, with the latter being a better predictor of ecosystem functions. Annual temperature, annual precipitation, and pH shaped (p < 0.050) both bacterial taxonomic and functional communities. By establishing linkages between bacterial taxonomic communities, abundances of bacterial functional groups, and soil CO2 fluxes, we provide novel insights into how soil bacterial communities could serve as potential proxies of ecosystem functions.

Long‐term degradation from marshes into meadows shifts microbial functional diversity of soil phosphorus cycling in an alpine wetland of the Tibetan Plateau

AbstractSoil microbes greatly contribute to the regulating of phosphorus (P) cycling, which plays a significant role in maintaining wetland ecosystem processes and function. The microbial functional diversity of soil P cycling in response to wetland degradation, however, remains largely unknown. We used metagenomic sequencing to investigate the microbial community and genes related to soil P cycling in un‐degraded marshes and meadows derived from long‐term marsh degradation in the Lalu alpine wetland of the Tibetan Plateau. When the marsh degraded into meadow, organic P (OP) mineralization genes increased while genes related to P‐starvation response regulation decreased. Proteobacteria (20.5–74.3%) and Actinobacteria (5.6–59.7%) were the dominant phyla in soils and were also the main contributors (39.7–84.1% in total) to soil P‐cycling genes. Soil pH was the primary factor influencing the P‐cycling functional genes. Soil pH negatively affected the genes related to the P‐uptake and transport system and had negative effects on the genes related to P‐starvation response regulation, OP mineralization, and inorganic P solubilization. These findings may deepen our understanding of the biogeochemical process of soil OP and may be beneficial for wetland management.

Difficult-to-culture bacteria in the rhizosphere: The underexplored signature microbial groups

Microorganisms represent a substantial portion of the earth's biodiversity and biomass, and the plant rhizosphere is an innate reservoir teeming with heterogeneous microbes predominated by bacterial communities. Rhizospheric microbial diversity (genetic, phenotypic, and metabolic) has been extensively studied to understand the key ecological roles played by the microbial members, including plant growth promotion. The application of 16S rRNA gene sequencing and next-generation sequencing (NGS) technologies has revolutionized the discovery of novel bacterial groups that have remained undetected by traditional cultivation-based approaches. Such technological advancements have opened new vistas in our current understanding of predominant but concealed and missed bacterial diversity referred to as difficult-to-culture bacterial lineages, especially the predominant phyla Acidobacteria, Verrucomicrobia, Planctomycetes, and Gemmatimonadetes. Regardless of their ubiquity and prevalence, little is known about their ecophysiology because of the non-availability of culturable members. More recently, there has been increased interest in understanding the cosmopolitan distribution and diversity of the difficult-to-culture bacteria, focusing on their role in driving complex plant-microbial interactions and mobilizing nutrients in soil and their potential as sources of novel bioactive metabolites. As an initial step, we review the distribution and significance of such bacterial phyla in soil, their ecophysiological roles, and their hidden plant growth promoting potential. The ability to select and deploy plant probiotic bacteria from the difficult-to-culture fraction of the bacterial community might open new avenues for improving crop health.

Effects of different concentrations and types of microplastics on bacteria and fungi in alkaline soil

The threat of microplastic (MP) pollution of soil ecosystems has aroused global concern; however, relatively few studies have focused on the effects of MPs on both bacterial and fungal communities in soil. In this study, a 310-day soil incubation experiment was designed to examine the effects of 7% and 14% (W/W) polyethylene (PE), polystyrene (PS), and polyvinyl chloride (PVC) MPs on soil enzyme activities and soil bacterial as well as fungal communities. The findings revealed that all three kinds of MPs stimulated soil enzyme activities, with 14% PVC, 7% PS, and 14% PE having the greatest impact on the activities of catalase, urease, and alkaline phosphatase. MPs did not change the types but the relative abundance of these phyla in soil. MPs mainly increased the abundance of Proteobacteria, Actinobacteria, and Ascomycota as well as declined the abundance of Acidobacteria, Basidiomycota, and Chytridiomycota. The response of fungi to MPs was stronger than that of bacteria, and the diversity of fungal communities was more sensitive to the impact of MPs than that of bacterial communities. PVC had the greatest impact on the diversity of microbial communities. PICRUSt analysis revealed that MPs mainly promoted the metabolic function of soil bacteria. Based on the FUNGuid tool, it was found that MPs had significant effects on fungi, which were closely related to plant growth. These results indicate that the impact of MPs on soil microbial communities depends on the type and concentration of MPs and that bacteria and fungi are affected differently by MPs. Future studies could be focused on the different effects of MPs on fungi and bacteria, and what effect will this difference have on plant growth.

Diverse compost products influence soil bacterial and fungal community diversity in a potato crop production system

Compost application may be an effective means to rapidly increase soil organic matter, soil quality, and soil microbial community diversity in intensive potato crop production systems. This study compared three contrasting compost products with a no compost control on soil chemical properties and soil bacterial and fungal community composition and diversity. The three composts consisted of municipal source separate waste compost (SSOC), forestry and poultry manure compost (FPMC), and forestry residues waste compost (FRC) with low, medium and high forestry waste percentages in their feedstock, respectively. Soil samples were collected on four dates over 11 months after compost application in October 2014. Soil pH, dissolved organic carbon and readily mineralizable C (respiration) were significantly greater in FPMC- and SSOC-treated soils compared to FRC-treated and control soils. Compost application influenced the relative abundances of several bacterial phyla in soils compared to control soils but not the relative abundances of fungal phyla. Several compost-borne bacterial (average of 383 operational taxonomic units (OTUs)) and fungal (average of 66 OTUs) species could be detected in soil throughout the following growing season after compost product application suggesting that these species succeeded in establishing in soils. The β-diversity of bacterial and fungal communities in soils differed significantly among treatments and sampling dates, indicating that the applied composts resulted in a change in the bacterial and fungal community diversity. Convergence of bacterial community diversity was observed among treatments over time but not for fungal community. The application of diverse compost products clearly changed the soil chemical properties which in turn influenced the bacterial and fungal communities. The effects of compost application on microbial communities were persistent, and could still be observed nearly a year after compost was applied.

Metagenomic analysis of the diversity of microbes in the Napahai plateau wetland and their carbon and nitrogen metabolisms

Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.

Transformation of Silver Nanoparticles (AgNPs) during Lime Treatment of Wastewater Sludge and Their Impact on Soil Bacteria.

This study investigated the impact of lime stabilization on the fate and transformation of AgNPs. It also evaluated the changes in the population and diversity of the five most relevant bacterial phyla in soil after applying lime-stabilized sludge containing AgNPs. The study was performed by spiking an environmentally relevant concentration of AgNPs (2 mg AgNPs/g TS) in sludge, applying lime stabilization to increase pH to above 12 for two hours, and applying lime-treated sludge to soil samples. Transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS) were used to investigate the morphological and compositional changes of AgNPs during lime stabilization. After the application of lime stabilized sludge to the soil, soil samples were periodically analyzed for total genomic DNA and changes in bacterial phyla diversity using quantitative polymerase chain reaction (qPCR). The results showed that lime treatment effectively removed AgNPs from the aqueous phase, and AgNPs were deposited on the lime molecules. The results revealed that AgNPs did not significantly impact the presence and diversity of the assessed phyla in the soil. However, lime stabilized sludge with AgNPs affected the abundance of each phylum over time. No significant effects on the soil total organic carbon (TOC), heterotrophic plate count (HPC), and percentage of the live cells were observed.

Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community.

The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alphadiversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were moresimilar, and Qm and Fm were also moresimilar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP).In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.

Effects of plant growth promoting Rhizobacteria microbial on the growth, rhizosphere soil properties, and bacterial community of Pinus sylvestris var. mongolica seedlings

ABSTRACT The use of plant growth promoting rhizobacteria (PGPR) instead of pesticides to promote plant growth has received widespread attention. In this study, potted experiments and high-throughput Illumina MiSeq sequencing technology were used to evaluate the effects of inoculation of three PGPR strains on the biomass of Pinus sylvestris var. mongolica and soil bacterial diversity. The results showed that the three PGPR strains all have the ability to secrete indole-3-acetic acid (IAA), dissolve inorganic phosphorus and produce siderophores. After inoculation with the PGPR strain, the plant seedling height increased significantly by 27.60%, and the root length increased significantly by 47.88% (P < 0.05), soil available nitrogen, phosphorus and potassium increased by 19.05%-47.62%, 26.63%-83.32% and 87.70%-98.10% respectively (P < 0.05). High-throughput sequencing results showed that the abundant bacterial phyla in soil include: Acidobacteria, Patescibacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Firmicutes, Actinobacteria, and Proteobacteria. The Monte-Carlo permutation test indicated that soil AP, TP, AK, and OM were the main environmental parameters influencing the composition of the microbial communities (at the genus level). This study provides basic data references for PGPR strains to improve the soil microecological environment and promote the growth and development of Pinus sylvestris var. mongolica seedlings.

Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes.

ABSTRACTMembers of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota. They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes’ epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria. We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.