Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest

Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.)

Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.

Subtle changes in topsoil microbial communities of drained forested peatlands after prolonged drought

A major consequence of anthropogenic climate change is the intensification and extension of drought periods. Prolonged drought can alter conditions in drained peatlands and cause disturbances in microbial communities in the topsoil layer of the peat. Varying environmental conditions throughout the growing season, such as the availability of organic matter and nutrients, temperature and water table, further impact these communities and consequently affect carbon and nutrient cycles. The impact of drought and new forestry practices is largely unknown in drained peatland forests. We examined how microbial communities change over a growing season in different harvesting intensities (continuous cover forestry, clear-cut and uncut) in a drained peatland site using bacterial 16S and fungal ITS2 rRNA analysis. We found seasonal differences in bacterial and fungal diversity and species richness, and subtle changes in microbial communities at the phylum and genus levels when comparing various environmental factors. Diversity, species richness and relative abundance differed in spring compared to summer and autumn. However, significant differences in the microbial community structure were not detected. Understanding the responses of microbial communities to disturbances like drought and other environmental factors provides new insights into the consequences of climate change on drained forested peatlands.

Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity

Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.

Soil Parameters and Forest Structure Commonly Form the Microbiome Composition and Activity of Topsoil Layers in Planted Forests

Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples' respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.

Sequential oxidation-composting-phytoremediation treatment for the management of an oily sludge from petroleum refinery

Oily sludges are generated in large quantities in petroleum refinery wastewater treatment plants. Given their complex composition, they are classified as hazardous waste. Selecting a single treatment technique for their remediation is challenging. This work aims to assess the extent of composting followed by phytoremediation on an oily sludge from an API separator unit, pre-treated by chemical oxidation with alkaline activated persulfate (PS). 18% of total petroleum hydrocarbons (TPH) were determined by IR spectroscopy. The aliphatic hydrocarbon content was 4714 ± 250 ppm by GC-FID, and aromatics were not detectable, suggesting a high amount of non-chromatographable complex hydrocarbons. The density of generalist and hydrocarbon-degrading populations of the oily sludge estimated by quantitative polymerase chain reaction (qPCR) evidenced an autochthonous microbiota with hydrocarbon-degrading capacity. The oxidative treatment with PS removed 31% of the TPH determined by IR after 20 days. The significant reduction of the native bacterial community was counterbalanced by coupling a composting treatment. Co-composting the sludge with goat manure and oat straw produced, after a year, a 96% reduction in TPH content, regardless of the oxidative pretreatment. Organic matter transformation was evidenced by the decrease of dissolved organic carbon (DOC) and the variation in E4/E6 ratio. The matrices obtained of composting were used as substrates for phytoremediation for 4 months. Ryegrass seeds were planted in both PS-treated and untreated sludge substrates. The presence of the plant grown in the pre-oxidised and composted substrate resulted in a higher aerial biomass of ryegrass (67%), an increase in enzymatic activities, and higher concentration of DOC, although without evidence of additional dissipation of TPH. The dynamics of the bacterial communities of the different substrates generated during the biological treatment were analyzed by Illumina NovaSeq DNA sequencing of 16S rRNA amplicons. The findings mirrored a succession compatible with that described in contaminated matrices, but also in other non-contaminated ones. According to these findings, an organic matter transformation process occurred, which included the complex hydrocarbons of the oily sludge, resulting in an active substrate that promoted the retention of nutrients and water and provided the necessary support for plant development.

Incidence of resistance to ALS and ACCase inhibitors in Echinochloa species and soil microbial composition in Northern Italy

The increasing amount of weeds surviving herbicide represents a very serious problem for crop management. The interaction between microbial community of soil and herbicide resistance, along with the potential evolutive consequences, are still poorly known and need to be investigated to better understand the impact on agricultural management. In our study, we analyzed the microbial composition of soils in 32 farms, located in the Northern Italy rice-growing area (Lombardy) with the aim to evaluate the relationship between the microbial composition and the incidence of resistance to acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase) inhibiting herbicides in Echinochloa species. We observed that the coverage of weeds survived herbicide treatment was higher than 60% in paddy fields with a low microbial biodiversity and less than 5% in those with a high microbial biodiversity. Fungal communities showed a greater reduction in richness than Bacteria. In soils with a reduced microbial diversity, a significant increase of some bacterial and fungal orders (i.e. Lactobacillales, Malasseziales and Diaporthales) was observed. Interestingly, we identified two different microbial profiles linked to the two conditions: high incidence of herbicide resistance (H-HeR) and low incidence of herbicide resistance (L-HeR). Overall, the results we obtained allow us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence based on the composition of the soil microbiome and especially on the degree of biodiversity of the microbial communities.

Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production

Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.

Decoding seasonal changes: soil parameters and microbial communities in tropical dry deciduous forests

In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.

Root Exposure of Graphitic Carbon Nitride (g-C3N4) Modulates Metabolite Profile and Endophytic Bacterial Community to Alleviate Cadmium- and Arsenate-Induced Phytotoxicity to Rice (Oryza sativa L.)

To investigate the mechanisms by which g-C3N4 alleviates metal(loid)-induced phytotoxicity, rice seedlings were exposed to 100 and 250 mg/kg graphitic carbon nitride (g-C3N4) with or without coexposure to 10 mg/kg Cd and 50 mg/kg As for 30 days. Treatment with 250 mg/kg g-C3N4 significantly increased shoot and root fresh weight by 22.4-29.9%, reduced Cd and As accumulations in rice tissues by 20.6-26.6%, and elevated the content of essential nutrients (e.g., K, S, Mg, Cu, and Zn) compared to untreated controls. High-throughput sequencing showed that g-C3N4 treatment increased the proportion of plant-growth-promoting endophytic bacteria, including Streptomyces, Saccharimonadales, and Thermosporothrix, by 0.5-3.30-fold; these groups are known to be important to plant nutrient assimilation, as well as metal(loid) resistance and bioremediation. In addition, the population of Deinococcus was decreased by 72.3%; this genus is known to induce biotransformation As(V) to As(III). Metabolomics analyses highlighted differentially expressed metabolites (DEMs) involved in the metabolism of tyrosine metabolism, pyrimidines, and purines, as well as phenylpropanoid biosynthesis related to Cd/As-induced phytotoxicity. In the phenylpropanoid biosynthesis pathway, the increased expression of 4-coumarate (1.13-fold) and sinapyl alcohol (1.26-fold) triggered by g-C3N4 coexposure with Cd or As played a critical role in promoting plant growth and enhancing rice resistance against metal(loid) stresses. Our findings demonstrate the potential of g-C3N4 to enhance plant growth and minimize the Cd/As-induced toxicity in rice and provide a promising nanoenabled strategy for remediating heavy metal(loid)-contaminated soil.

Differences in microbial community structure and metabolic activity among tea plantation soils under different management strategies

Introduction

Microorganisms play an important role in the multifunctionality of soil ecosystems. Soil microbial diversity and functions have a great impact on plant growth and development. The interactions between tea trees and soil microbiota can be linked with planting patterns and management strategies, whose effects on soil microbial community structure and metabolites are still unclear.

Methods

Here we used amplicon sequencing and metabolomic analysis to investigate the differences in soil microbial composition and metabolites among three tea production systems: organic, non-organic, and intercropping.

Results

We detected significant differences among the three systems and found that Firmicutes, Proteobacteria, Acidobacteriota, Actinobacteriota and Chloroflexi were the main bacteria in the three soil groups, although they varied in relative abundance. Acidobacteria bacterium increased significantly in the organic and intercropping groups. For fungi, Ascomycota and Basidiomycota were the main differential fungal phyla. Fungi alpha-diversity in the non-organic group was significantly higher than that in the other two groups, and was correlated with multiple soil physical and chemical factors. Moreover, network analysis showed that bacteria and fungi were strongly correlated. The changes in soil microorganisms caused by management and planting patterns may affect soil quality through corresponding changes in metabolites. Metabolomic analysis showed differences in metabolite composition among different groups. It was also found that the arachidonic acid metabolic pathway was affected by changes in soil microorganisms, and may further affect soil quality in an essential manner.

Discussion

Planting patterns and management strategies may significantly affect soil microorganisms and therefore metabolites. Changes in soil microorganisms, especially in fungi, may alter soil quality by affecting soil physicochemical properties and metabolites. This study will provide new insights into soil quality monitoring from a microbiological perspective.

Short-chain fatty acid production and phosphorous recovery from waste activated sludge via anaerobic fermentation: A comparison of in-situ and ex-situ thiosulfate-assisted Fe2+/persulfate pretreatment

Recently, increasing attention is given on the resource and energy recovery (e.g. short-chain fatty acids (SCFAs) and phosphorus (P)) from waste active sludge (WAS) under the "Dual carbon goals". This study compared four thiosulfate-assisted Fe²⁺/persulfate (TAFP) pretreatments of WAS, i.e. in-situ TAFP pretreatment (R1), ex-situ TAFP pretreatment (R2), in-situ TAFP pretreatment + pH adjustment (R3) and ex-situ TAFP pretreatment + pH adjustment (R4), followed by anaerobic fermentation over 20 days for SCFA production and P recovery. The results showed that the maximal SCFA yields in R1-4 were 730.2 ± 7.0, 1017.4 ± 13.9, 860.1 ± 40.8, and 1072.0 ± 33.2 mg COD/L, respectively, significantly higher than Control (365.2 ± 17.8 mg COD/L). The findings indicated that TAFP pretreatments (particularly ex-situ TAFP pretreatment) enhanced WAS disintegration and provided more soluble organics and subsequently promoted SCFA production. The P fractionation results showed the non-apatite inorganic P increased from 11.6 ± 0.2 mg P/g TSS in Control to 11.8 ± 0.5 (R1), 12.4 ± 0.3 (R2), 13.2 ± 0.7 (R3) and 12.7 ± 0.7 mg P/g TSS (R4), suggesting TAFP pretreatments improved P bioavailability due to formation of Fe-P mineral (Fe(H₂PO₄)₂·2H₂O), which could be recycled through magnetic separators. These findings were further strengthened by the analysis of microbial community and related marker genes that fermentative bacteria containing SCFA biosynthesis genes (e.g. pyk, pdhA, accA and accB) and iron-reducing bacteria containing iron-related proteins (e.g. feoA and feoB) were enriched in R1-4 (dominant in ex-situ pretreatment systems, R2 and R4). Economic evaluation further verified ex-situ TAFP pretreatment was cost-effective and a better strategy over other operations to treat WAS for SCFA production and P recovery.

The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests

Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.

Application of Sophora alopecuroides organic fertilizer changes the rhizosphere microbial community structure of melon plants and increases the fruit sugar content

BACKGROUND

Sophora alopecuroides L. is a leguminous plant commonly found in northwest China. In Xinjiang, the fresh herb of S. alopecuroides is often applied as a green fertilizer to the rhizosphere of melon (Cucumis melo) plants at the end of their flowering period, to improve the taste of the fruits. However, the effects of S. alopecuroides-based fertilizers on the microbial community structure of soil and crop-root systems are unclear. In order to study the sweetening mechanism of the S. alopecuroides organic fertilizer, three different varieties of melon were selected. The untreated plants were used as the control (CK) group, and the plants treated with S. alopecuroides-based organic fertilizer were selected as the treatment (T) group. The physical and chemical properties, enzyme activities and microbial community structure of the rhizosphere samples were also determined, and a correlation analysis with the fruit sweetness index was conducted.

RESULTS

Sugar content of group T was at least 40% higher than that of group CK. The increase in fruit sugar content positively correlated with the increase in the abundance of beneficial microorganisms, including Pseudomonas, Bacillus, Mycobacterium, Burkholderia, Streptomyces, Acinetobacter, Proteobacteria, Lysobacter, Actinomycetes, Penicillium and Aspergillus.

CONCLUSION

Sophora alopecuroides organic fertilizer could alter the composition and function of bacterial and fungal communities and promote the growth of beneficial bacteria in the melon plant rhizosphere. Further, it could increase the content of soluble solids and sugar in the fruits to achieve a sweetening effect. This fertilizer can be applied as a fruit sweetener in melon cultivation, improving the sugar content of the fruit and consequently the sweetness. © 2022 Society of Chemical Industry.

Effective degradation of organophosphate ester flame retardants and plasticizers in coastal sediments under high urban pressure

Empirical evidence of the effective degradation at environmentally relevant conditions of organophosphate esters (OPEs) flame retardants and plasticizers in coastal sediments from an impacted area in the NW Mediterranean Sea is provided. Half-lives varied from 23.3 to 77.0 (abiotic conditions) and from 16.8 to 46.8 days (biotic conditions), depending on the compound, highlighting the relevant role of microbial assemblages enhancing OPE degradation. After an immediate significant reduction of the bacterial abundance due to OPE addition to the sediment at the very beginning of the experiment, the observed biodegradation was associated to a general stimulation of the growth of the bacterial community during a first period, but without a marked change of the structure of the community. However, OPE contamination induced a decrease on the diversity of the bacterial community in the coastal sediment, noticeable after 14 days of incubation. It is likely that on one side the contamination had favoured the growth of some bacterial groups maybe involved in the biodegradation of these compounds but, on the other side, had also impacted some sensitive bacteria. The estimated half-lives fill a data gap concerning OPE degradation rates in marine sediments and will be valuable data for the refinement of OPE chemical risk assessment in marine environments, particularly on impacted sites.

Community-integrated multi-omics facilitates screening and isolation of the organohalide dehalogenation microorganism

A variety of anthropogenic organohalide contaminants generated from industry are released into the environment and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by metagenomic sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavob a cteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 metagenome-assembled genomes were identified, suggesting that the potential for organohalide hydrolytic dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.

Research of cervical microbiota alterations with human papillomavirus infection status and women age in Sanmenxia area of China

Background

Human papillomavirus (HPV) infection is the leading cause of cervical cancer. More and more studies discovered that cervical microbiota (CM) composition correlated with HPV infection and the development of cervical cancer. However, more studies need to be implemented to clarify the complex interaction between microbiota and the mechanism of disease development, especially in a specific area of China.

Materials and methods

In this study, 16S rDNA sequencing was applied on 276 Thin-prep Cytologic Test (TCT) samples of patients from the Sanmenxia area. Systematical analysis of the microbiota structure, diversity, group, and functional differences between different HPV infection groups and age groups, and co-occurrence relationships of the microbiota was carried out.

Results

The major microbiota compositions of all patients include Lactobacillus iners, Escherichia coli, Enterococcus faecalis, and Atopobium vaginae at species level, and Staphylococcus, Lactobacillus, Gardnerella, Bosea, Streptococcus, and Sneathia in genus level. Microbiota diversity was found significantly different between HPV-positive (Chao1 index: 98.8869, p < 0.01), unique-268 infected (infections with one of the HPV genotype 52, 56, or 58, 107.3885, p < 0.01), multi-268 infected (infections with two or more of HPV genotype 52, 56, and 58, 97.5337, p = 0.1012), other1 (94.9619, p < 0.05) groups and HPV-negative group (83.5299). Women older than 60 years old have higher microbiota diversity (108.8851, p < 0.01, n = 255) than younger women (87.0171, n = 21). The abundance of Gardnerella and Atopobium vaginae was significantly higher in the HPV-positive group than in the HPV-negative group, while Burkholderiaceae and Mycoplasma were more abundant in the unique-268 group compared to the negative group. Gamma-proteobacteria and Pseudomonas were found more abundant in older than 60 patients than younger groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) analysis revealed the effects on metabolism by microbiota that the metabolism of cells, proteins, and genetic information-related pathways significantly differed between HPV-negative and positive groups. In contrast, lipid metabolism, signal transduction, and cell cycle metabolism pathway significantly differed between multi-268 and negative groups.

Conclusion

The HPV infection status and age of women were related to CM’s diversity and function pathways. The complex CM co-occurrent relationships and their mechanism in disease development need to be further investigated.

Effects of Tetracycline and Copper on Water Spinach Growth and Soil Bacterial Community

The effects of tetracycline (TC) and copper (Cu) on the growth of water spinach and the bacterial community structure in soil were examined in this study. The results revealed that a single Cu treatment decreased water spinach development more severely than TC, and that the toxic effects of TC and Cu on water spinach were synergistic at low doses and antagonistic at high concentrations. The single Cu treatment had the largest influence on the activities of three antioxidant enzymes (Superoxide Dismutase (SOD), Peroxidase (POD), Catalase (CAT)) and the content of Malondialdehyde (MDA) in water spinach leaves, followed by the TC and Cu composed treatment, with the single TC treatment having the least effect. The results of 16Sr RNA sequence analysis showed that the richness and diversity of soil bacterial communities were reduced by either a single TC or Cu treatment. Cu had a greater effect on the composition of the microbial community at genus level than TC. In conclusion, Cu had a greater influence on the growth of water spinach and soil microbial community composition than TC. TC and Cu exhibited synergistic effects at low concentrations and antagonistic effects at high concentrations on relevant indicators when Cu concentration was fixed.

Bacterial Communities in the Fruiting Bodies and Background Soils of the White Truffle Tuber magnatum

Tuber magnatum Picco is a greatly appreciated truffle species mainly distributed in Italy. Its price and characteristics mostly depend on its geographical origin. Truffles represent a fundamental step of the life cycle of Tuber species promoting spore dissemination. They consist of two main parts, gleba, the inner part, and peridium, which is in direct contact with ground soil. Within the truffle and around in the growing soil, both the occurrence and abundance of different microbial species seem to play an essential role in truffle production. The development of the next-generation sequencing (NGS) based technology has greatly improved to deepen the role of the composition of microbial communities, thus improving the knowledge of the existing relationships between microbial taxa in a specific condition. Here, we applied a metabarcoding approach to assess the differences in T. magnatum samples collected from three areas in Tuscany (Italy). Peridium and gleba were analyzed separately with the aim to distinguish them based on their microbial composition. Also, soil samples were collected and analyzed to compare productive and unproductive truffle grounds to confirm the presence of specific patterns linked to truffle production. Results indicate that differences occurred between truffle compartments (gleba and peridium) as well as between analyzed soils (productive and unproductive), with distinctive taxa associated. Furthermore, findings also demonstrated specific characteristics associated with truffle collection areas, thus indicating a degree of microbial selection related to different environments.

The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient

Background

Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing.

Results

The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected.

Conclusions

In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment.

Significance and impact of the study

Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02496-z.

Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake

The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.

Response of constructed wetland for wastewater treatment to graphene oxide: Perspectives on plant and microbe

The wide application of graphene oxide (GO) increases its release into environment with less known on environmental effects. This work investigated 120-day interaction between GO (500 and 5000 μg/L) and constructed wetlands (CWs) planted with Iris pseudacorus. CWs showed the effective retention for GO via mature biofilm but less biodegradation. GO significantly induced enzyme activities (urease, neutral phosphatase, and catalase), which was attributed to increases in ecological association and enzyme abundance. GO decreased microbial biomass on day 30, but it had no impacts on day 120. The microbial community showed gradual self-adaption with time due to protection of antioxidant defense system (L-ascorbate oxidase, superoxide reductase, and glutathione related enzyme). The antioxidant enzymes (superoxide dismutase and peroxidase) and lipid peroxidation of Iris pseudacorus were increased by GO, accompanied by reduction on chlorophyll biosynthesis. Overall, the separate effects of GO on micro-regions and individual bodies in CWs were obvious, but it was acceptable that variations in pollutant removal were not evident due to synergetic role of plant-substrate-microbe. Organic matter and phosphorus removals reached to above 93%, and ammonia and total nitrogen removals in GO groups were reduced by 7-8% and 9-13%, respectively.

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes

Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling.

IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.

Soil Layers Matter: Vertical Stratification of Root-Associated Fungal Assemblages in Temperate Forests Reveals Differences in Habitat Colonization

Ectomycorrhizal and saprotrophic fungi play pivotal roles in ecosystem functioning. Here, we studied the vertical differentiation of root-associated fungi (RAF) in temperate forests. We analysed RAF assemblages in the organic and mineral soil from 150 experimental forest plots across three biogeographic regions spanning a distance of about 800 km. Saprotrophic RAF showed the highest richness in organic and symbiotrophic RAF in mineral soil. Symbiotrophic RAF exhibited higher relative abundances than saprotrophic fungi in both soil layers. Beta-diversity of RAF was mainly due to turnover between organic and mineral soil and showed regional differences for symbiotrophic and saprotrophic fungi. Regional differences were also found for different phylogenetic levels, i.e., fungal orders and indicator species in the organic and mineral soil, supporting that habitat conditions strongly influence differentiation of RAF assemblages. Important exceptions were fungal orders that occurred irrespective of the habitat conditions in distinct soil layers across the biogeographic gradient: Russulales and Cantharellales (ectomycorrhizal fungi) were enriched in RAF assemblages in mineral soil, whereas saprotrophic Polyporales and Sordariales and ectomycorrhizal Boletales were enriched in RAF assemblages in the organic layer. These results underpin a phylogenetic signature for niche partitioning at the rank of fungal orders and suggest that RAF assembly entails two strategies encompassing flexible and territorial habitat colonization by different fungal taxa.