Chao1 Richness Research Articles

Impact of antibiotics, iron oxide, and sodium sulfate on microbial community composition in laboratory-built municipal solid waste microcosms.

Municipal solid waste (MSW) landfills represent underexplored microbial ecosystems. Landfills contain variable amounts of antibiotic and construction and demolition (C&D) wastes, which have the potential to alter microbial metabolism due to biocidal or redox active components, and these effects are largely underexplored. To circumvent the challenge of MSW heterogeneity, we conducted a 65-day time series study on simulated MSW microcosms to assess microbiome changes using 16S rRNA sequencing in response to 1) Fe(OH)3 and 2) Na2SO4 to represent redox active components of C&D waste as well as 3) antibiotics. The addition of Fe(OH)3 altered the overall community composition and increased Shannon diversity and Chao1 richness. The addition of a mixture of seven antibiotics (1000 ng/L each) altered the community composition without affecting diversity metrics. Sulfate addition had little effect on microbial community composition or diversity. These results suggest that the microbial community composition in fresh MSW may be significantly impacted by influxes of iron waste and a single application of antibiotics.

Tree species-dependent effects of afforestation on soil fungal diversity, functional guilds and co-occurrence networks in northern China

Afforestation exerts a profound impact on soil fungal communities, with the nature and extent of these changes significantly influenced by the specific tree species selected. While extensive research has addressed the aboveground ecological outcomes of afforestation, the nuanced interactions between tree species and soil fungal dynamics remain underexplored. This study investigated the effects of afforestation with Caragana microphylla (CMI), Populus simonii (PSI), and Pinus sylvestris var. mongolica (PSY) on soil fungal diversity, functional guilds, and co-occurrence networks, drawing comparisons with neighboring grasslands. Our findings reveal a significant increase in soil fungal Chao1 richness following afforestation, though the degree of enhancement varied across tree species. Specifically, CMI and PSI forests showed notable increases in fungal richness, whereas the response in PSY forests was comparatively modest. Saprotrophic fungal groups, integral to organic matter decomposition, showed a substantial increase across all afforested sites, with CMI forests exhibiting an impressive 205.58% rise. Conversely, pathogenic fungi, which can negatively impact plant health, demonstrated a marked decrease within plantation forests. Symbiotic groups, particularly ectomycorrhizal fungi, were notably enriched solely in PSI forests. Co-occurrence network analysis further indicated that afforestation alters fungal network complexity: CMI forests displayed increased network interactions, while PSI and PSY forests exhibited a reduction in network connectivity. Soil bulk density and organic carbon content emerged as key factors influencing network complexity, whereas tree species identity played a crucial role in shaping soil fungal community composition. Collectively, these results emphasize the importance of adopting a species-specific strategy for afforestation to optimize soil fungal diversity and network structure, ultimately enhancing the ecological resilience and sustainability of forest plantation ecosystems.

Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management.

Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments.

Interaction Effects of Vegetation and Soil Factors on Microbial Communities in Alpine Steppe Under Degradation

To clarify the regulating effect of vegetation and soil factors on microbial communities in the alpine steppe under degradation on the Qinghai-Xizang Plateau, the alpine steppe in the Sanjiangyuan area of the Qinghai-Tibet Plateau was chosen. We analyzed the differences in vegetation and soil factors in different stages of degradation （non-degradation, moderate degradation, and severe degradation） and detected the variations in microbial community characteristics in the alpine steppe under different degradation stages using high-throughput sequencing technology. Eventually, redundancy analysis （RDA） and multiple regression matrixes （MRM） based on the similarity or dissimilarity matrix were used to identify key environmental factors regulating microbial （bacterial and fungal） community changes under degradation. The results showed that the degradation of the alpine steppe significantly changed the community coverage, height, biomass, and important value of graminae； significantly reduced the contents of soil organic matter, total nitrogen, total phosphorus, and silt； and increased the soil bulk density and sand content. Degradation did not change the composition of bacteria and fungi, but their composition proportions changed and also resulted in the loss of microbial richness （Chao1 index and Richness index） but did not significantly change the microbial diversity （Shannon index）. With the occurrence of degradation, the vegetation characteristics, soil physicochemical properties, and microbial diversity showed a consistent change trend. Combined with the characteristics of the network topology changes （the number of nodes and clustering coefficient significantly decreased）, it was found that degradation of the alpine steppe led to the decline of interspecies interactions, decentralization of network, and homogenization of microorganisms, but the cooperation relations among the species were maintained （positive correlation connections accounted for more than 90% in all degradation stages）. Under the alpine steppe degradation, the vegetation-soil interaction had the greatest effect on soil bacterial community, whereas soil physicochemical properties had the greatest influence on soil fungal community. Specifically, vegetation community height, biomass, and soil bulk density were the mutual factors regulating soil microorganisms, whereas the vegetation Simpson index, important value of graminae, soil total phosphorus, total potassium, and silt content were the unique factors affecting the soil bacterial community, and soil pH and total nitrogen content were the particular factors affecting the soil fungal community.

Bacterial community in the buckwheat rhizosphere responds more sensitively to single microplastics in lead-contaminated soil compared to the arbuscular mycorrhizal fungi community

Soil pollution by microplastics (MPs), defined as plastic particles <5 mm, and heavy metals is a significant environmental issue. However, studies on the co-contamination effects of MPs and heavy metals on buckwheat rhizosphere microorganisms, especially on the arbuscular mycorrhizal fungi (AMF) community, are limited. We introduced low (0.01 g kg−1) and high doses of lead (Pb) (2 g kg−1) along with polyethylene (PE) and polylactic acid (PLA) MPs, both individually and in combination, into soil and assessed soil properties, buckwheat growth, and rhizosphere bacterial and AMF communities in a 40-day pot experiment. Notable alterations were observed in soil properties such as pH, alkaline hydrolyzable nitrogen (AN), and the available Pb (APb). High-dose Pb combined with PLA-MPs hindered buckwheat growth. Compared to the control, bacterial Chao1 richness and Shannon diversity were lower in the high dose Pb with PLA treatment, and differentially abundant bacteria were mainly detected in the high Pb dose treatments. Variations in bacterial communities correlated with APb, pH and AN. Overall, the AMF community composition remained largely consistent across all treatments. This phenomenon may be due to fungi having lower nutritional demands than bacteria. Stochastic processes played a relatively important role in the assembly of both bacterial and AMF communities. In summary, MPs appeared to amplify both the positive and negative effects of high Pb doses on the buckwheat rhizosphere bacteria.

Comparative High-Throughput Sequencing Analysis of the Bacterial Community Associated with the Rhizosphere of Date Palm (Phoenix dactyllifera L.) Irrigated with Treated Wastewater and Groundwater

Water scarcity is a major agricultural issue in most arid and semi-arid regions of the world. Alternative water supplies, such as the reuse of wastewater for agricultural irrigation, have been introduced. However, little is known about their impact on the soil and rhizosphere microbiomes that receive irrigation. Therefore, this work evaluates the impact of treated wastewater (TWW) irrigation on the soil and rhizosphere bacterial communities of date palms in Al Madinah, Saudi Arabia. In this study, metagenomic DNA from the rhizosphere of the date palm was sequenced using Illumina high-throughput sequencing. According to the observed OTUs, Chao1 richness estimations, and Shannon diversity values, soils from groundwater-irrigated date palms showed higher microbial diversity than did soils from TWW-irrigated date palms. A total of 569 OTUs were generated; most of them (97.3%) were assigned into 15 different phyla, whereas 2.7% were marked as unclassified. DNA sequence analysis of the WWT-irrigated rhizosphere showed that the most abundant phyla were Firmicutes (43.6%), Bacteroidetes (17.3%), Proteobacteria (15.2%), and Actinobacteria (14.6%), representing more than 90.7% of the total community, while the soil of the rhizosphere irrigated with GW was dominated by Actinobacteria (44.1%), Proteobacteria (23.4%), Firmicutes (15.5%), and Gemmatimonadetes (4.9%). The most frequently observed species in the two soils were also different. The dominant species in TWW-irrigated soil was Planococcus plakortidis, which is prevalent in saline and moderately saline habitats and can play an important ecological role. The GW-irrigated rhizosphere exhibited higher levels of biocontrol bacteria, particularly Nocardioides mesophilus. These results provide a comprehensive understanding and insights into the population dynamics and microbiome of date palm rhizosphere. The findings show that the irrigation water quality has a significant impact on the microbiome composition. Identifying the microbial diversity is the first step toward determining the best way to use TWW in irrigation.

Unveiling hidden bacterial players: A closer look at the succession characteristics and co-occurrence patterns of abundant, intermediate and rare bacteria in biological soil crusts

The bacterial communities of biological soil crusts (BSCs) often comprise abundant, intermediate and rare taxa that form complex ecosystems through interspecies interactions and play essential roles in regulating the process of vegetative restoration. However, the community structure of nonabundant bacteria and the interactions among these abundance categories are still largely unknown. In light of this, we used Illumina MiSeq sequencing to investigate the succession characteristics and co-occurrence patterns of abundant bacteria (ABs), intermediate bacteria (IBs) and rare bacteria (RBs) in the three developmental stages of BSCs (cyanobacteria-, lichen- and moss-dominated crusts) on the southeastern edge of the Tengger Desert. The results showed that the changes in the Chao richness and taxonomic composition of ABs, IBs and RBs were significantly different during BSC succession. The results of the co-occurrence network analysis revealed that most of the observed associations were between RBs (more than 80 %), positive correlations were predominant (more than 77 %), and the vast majority of the keystone taxa in the BSC bacterial networks were RBs (only one belonged to IBs). Moreover, the driving effects of environmental variables on ABs, IBs and RBs were not exactly the same, and their diversity was a key driver of the co-occurrence network properties of the BSCs. These findings are crucial for understanding the establishment and maintenance of BSC bacterial diversity and provide a new perspective for utilizing microbial resources and/or regulating environmental factors to achieve the sustainable development of desert ecosystems.

Community responses of arbuscular mycorrhiza fungi to hydrological gradients in a riparian Phragmites australis wetland.

The hydrological regime is considered to be the major factor that affects the distribution of arbuscular mycorrhiza (AM) fungi in wetlands. We aimed to investigate the responses of AM fungal community to different hydrological gradients. Illumina Miseq sequencing technology was used to study the AM fungal community structure in roots and rhizosphere soils of Phragmites australis in different moisture areas (dry area, alternating wet and dry area, and flooded area) in Mengjin Yellow River wetland. The rhizosphere soils and roots hosted different AM fungal communities. In roots, the AM fungal colonization and Chao1 richness in dry area were significantly higher than that in alternating wet and dry area and flooded area, but the community composition did not vary clearly under different water conditions. In rhizosphere soils, the Chao1 richness of AM fungi in flooded area was significantly higher than that in alternating wet and dry area and dry area, and the AM fungal community structure obviously differed across different areas. The redundancy analyses indicated that changes in the AM fungal community in soils were associated with altered soil properties, and the abundance of the dominant genus Glomus was mostly positively correlated with alkali-hydrolyzable nitrogen in soils. This study helps us to understand the responses of AM fungal community to hydrological gradients in wetlands.

Soil bacterial community in a photovoltaic system adopted different survival strategies to cope with small-scale light stress under different vegetation restoration modes.

Solar photovoltaic (PV) power generation is a major carbon reduction technology that is rapidly developing worldwide. However, the impact of PV plant construction on subsurface microecosystems is currently understudied. We conducted a systematic investigation into the effects of small-scale light stress caused by shading of PV panels and sampling depth on the composition, diversity, survival strategy, and key driving factors of soil bacterial communities (SBCs) under two vegetation restoration modes, i.e., Euryops pectinatus (EP) and Loropetalum chinense var. rubrum (LC). The study revealed that light stress had a greater impact on rare species with relative abundances below 0.01% than on high-abundance species, regardless of the vegetation restoration pattern. Additionally, PV shadowing increased SBCs' biomass by 20-30% but had varying negative effects on the numbers of Operational Taxonomic Unit (OTU), Shannon diversity, abundance-based coverage estimator (ACE), and Chao1 richness index. Co-occurrence and correlation network analysis revealed that symbiotic relationships dominated the key SBCs in the LC sample plots, with Chloroflexi and Actinobacteriota being the most ecologically important. In contrast, competitive relationships were significantly increased in the EP sample plots, with Actinobacteriota having the most ecological importance. In the EP sample plot, SBCs were found to be more tightly linked and had more stable ecological networks. This suggests that EP is more conducive to the stability and health of underground ecosystems in vulnerable areas when compared with LC. These findings offer new insights into the effects of small-scale light stress on subsurface microorganisms under different vegetation restoration patterns. Moreover, they may provide a reference for optimizing ecological restoration patterns in fragile areas.

Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department

ObjectiveLittle is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage. MethodsWe conducted a case–control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity. ResultsParticipants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27–44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini–Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray–Curtis dissimilarity index, p 0.42). DiscussionIn this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.

Trichoderma spp. promotes ginseng biomass by influencing the soil microbial community.

Ginseng (Panax ginseng C.A. Meyer) has multiple effects on human health; however, soil degradation seriously affects its yield. Trichoderma spp. play an important role in improving plant biomass by influencing the soil environment. Therefore, it is necessary to screen efficient Trichoderma strains that can increase ginseng biomass and determine their mechanisms. Herein, we selected six Trichoderma species (T. brevicompactum, T. velutinum, T. viridescens, T. atroviride, T. koningiopsis, and T. saturnisporum) isolated from ginseng rhizosphere soil, and evaluated their growth promoting effects on ginseng and their influence on the microbiome and chemical attributes of the ginseng rhizosphere soil. Except for T. saturnisporum (F), compared with the control, the other five species increased ginseng biomass. In terms of chemical properties, the pH value, available potassium content, and available phosphorus content in the ginseng rhizosphere soil increased by 1.16-5.85%, 0.16-14.03%, and 3.92-38.64%, respectively, after root irrigation with spores of Trichoderma species. For the soil microbiome, fungal Chao1 and Ace richness indices decreased. Application of Trichoderma enhanced the relative level of Proteobacteria, but reduced the relative level of Ascomycota. At the genus level, application of Trichoderma enhanced the relative levels of Sphingomonas, Blastomonas, and Trichoderma, but reduced the relative level of Fusarium. Available K and available P were the most important elements that affected the structure of the bacterial community, while total K was the most influential element for the structure of the fungal community structure. The results indicated that the application of Trichoderma spp. could increase soil nutrients and regulate the structure and composition of the soil microbial community, thereby enhancing the biomass of ginseng. The results will provide guidance for soil improvement in ginseng cultivation.

Experiences of discrimination are associated with microbiome and transcriptome alterations in the gut.

Discrimination is a recognized psychosocial stressor that has been linked to various negative health outcomes. This study explored the impact of discrimination on gut health, specifically focusing on microbiome changes, predicted metagenomic differences, transcriptomic profiles, and the potential for using a multi-omic approach to predict discrimination to identify discrimination status for an individual. Methods: We conducted a comprehensive investigation involving male and premenopausal female participants, using the Everyday Discrimination Scale to classify them into either high or low discrimination. Multiple questionnaires were administered to evaluate participants' physiological, psychological, and perceived stressors. Two diet questionnaires were also administered. Stool samples were collected for microbiome analysis and RNA sequencing. Microbial composition changes were analyzed using the Shannon index and Chao1 richness estimator for alpha diversity and the Aitchison distance metric for beta diversity. Differential abundance was evaluated using MaAsLin2, followed by metatranscriptomics sequencing and annotation. A multi-omic approach utilizing random forest was used to assess the predictability of discrimination. The study results showed that high discrimination was linked to higher gut microbiome species richness (Chao1, p = 0.02) and significant beta diversity differences (p = 0.04). Prevotella and Ruminococcaceae were both less abundant in the high discrimination group. High discrimination participants also reported higher levels of depression, anxiety, perceived stress, early life adversity, visceral sensitivity, and neuroticism than those in the low discrimination group. Gene expression analysis revealed distinctive patterns, with significant changes in genes associated with environmental sensing (two-component system) and metabolic pathways. In a plot comparing gene transcription to DNA content, certain genes showed higher expression levels in participants who experienced both high and low levels of discrimination. Our random forest classifier demonstrated the capability to accurately differentiate individuals with high and low discrimination in our training cohort (AUC = 0.91). These findings illuminate the substantial impact of discrimination on gut health, encompassing microbiome composition, gene expression, and functional pathways. These findings suggest that discrimination is associated with internal biological changes that can be associated with negative health outcomes, opening research to examine novel pathways that can be used to mitigate the negative health effects of discrimination.

Endophytic bacteria in the periglacial plant Potentilla fruticosa var. albicans are influenced by habitat type

BackgroundMicrobial communities in different plant compartments are relatively independent entities. However, the influence of environmental factors on the microbial community in different compartments of periglacial plants remains unclear. In this study, we quantified the bacterial communities in the rhizosphere soil, as well as root and leaf endosphere compartments of a periglacial plant, Potentilla fruticosa var. albicans, using high-throughput DNA sequencing. Moreover, we evaluated the impacts of habitat types (glacier terminus zone, moraine ridge, and alpine meadow) on the bacterial community in different plant compartments of Potentilla fruticosa var. albicans.ResultsOur results showed that habitat type had a significant effect on the alpha diversity (Chao1 richness) of endophytic bacteria, but not on the rhizospheric bacteria. The community composition of rhizospheric and endophytic bacteria was significantly different across the three habitats, and habitat type had a greater effect on the endophytic bacteria than on rhizospheric bacteria. The contribution of rhizosphere soil to the root and leaf endophytes decreased with the transformation of habitats from glacier terminus zone to alpine meadow. In contrast, host selection pressure sequentially increased from the glacier terminus zone to the moraine ridge to the alpine meadow. Furthermore, we found that the bacterial co-occurrence network in the alpine meadow was more modular but had lower complexity and connectedness than that in the glacier terminus zone. The bacterial community was governed primarily by stochastic processes regardless of habitat type.ConclusionThis study reveals that the diversity and composition of endophytic bacteria associated with Potentilla fruticosa var. albicans are more affected by habitat types than that of rhizospheric bacteria. Our study also demonstrates that the assembly patterns and co-occurrence patterns of bacterial communities associated with Potentilla fruticosa var. albicans vary by habitat type. These results advance the current understanding of community assembly and ecological interactions of microbial communities associated with periglacial plants.

Associations of gut microbiome richness and diversity with objective and subjective sleep measures in a population sample.

Alterations in gut microbiota composition have been associated with several conditions, and there is emerging evidence that sleep quantity and quality are associated with the composition of the gut microbiome. Therefore, this study aimed to assess the associations between several measures of sleep and the gut microbiome in a large, population-based sample. Data were collected from participants in the Survey of the Health of Wisconsin from 2016 to 2017 (N = 720). Alpha diversity was estimated using Chao1 richness, Shannon's diversity, and Inverse Simpson's diversity. Beta diversity was estimated using Bray-Curtis dissimilarity. Models for each of the alpha-diversity outcomes were calculated using linear mixed effects models. Permutational multivariate analysis of variance tests were performed to test whether gut microbiome composition differed by sleep measures. Negative binomial models were used to assess whether sleep measures were associated with individual taxa relative abundance. Participants were a mean (SD) age of 55 (16) years and 58% were female. The sample was 83% non-Hispanic white, 10.6% non-Hispanic black, and 3.5% Hispanic. Greater actigraphy-measured night-to-night sleep duration variability, wake-after-sleep onset, lower sleep efficiency, and worse self-reported sleep quality were associated with lower microbiome richness and diversity. Sleep variables were associated with beta-diversity, including actigraphy-measured night-to-night sleep duration variability, sleep latency and efficiency, and self-reported sleep quality, sleep apnea, and napping. Relative abundance of several taxa was associated with night-to-night sleep duration variability, average sleep latency and sleep efficiency, and sleep quality. This study suggests that sleep may be associated with the composition of the gut microbiome. These results contribute to the body of evidence that modifiable health habits can influence the human gut microbiome.

Diversity and composition of microbial communities in Jinsha earthen site under different degree of deterioration

Earthen sites are the important cultural heritage that carriers of human civilization and contains abundant history information. Microorganisms are one of important factors causing the deterioration of cultural heritage. However, little attention has been paid to the role of biological factors on the deterioration of earthen sites at present. In this study, microbial communities of Jinsha earthen site soils with different deterioration types and degrees as well as related to environmental factors were analyzed. The results showed that the concentrations of Mg2+ and SO42− were higher in the severe deterioration degree soils than in the minor deterioration degree soils. The Chao1 richness and Shannon diversity indices of bacteria in different type deterioration were higher in the summer than in the winter; the Chao1 and Shannon indices of fungi were lower in the summer. The differences in bacterial and fungal communities were associated with differences in Na+, K+, Mg2+ and Ca2+ contents. Based on both the relative abundances in amplicon sequencing and isolated strains, the bacterial phyla Actinobacteria, Firmicutes and Proteobacteria, and the Ascomycota genera Aspergillus, Cladosporium and Penicillium were common in all soils. The OTUs enriched in the severe deterioration degree soils were mostly assigned to Actinobacteria and Proteobacteria, whereas the Firmicutes OTUs differentially abundant in the severe deterioration degree were all depleted. All bacterial isolates produced alkali, implying that the deterioration on Jinsha earthen site may be accelerated through alkali production. The fungal isolates included both alkali and acid producing strains. The fungi with strong ability to produce acid were mainly from the severe deterioration degree samples and were likely to contribute to the deterioration. Taken together, the interaction between soil microbial communities and environment may affect the soil deterioration, accelerate the deterioration process and threaten the long-term preservation of Jinsha earthen site.

Lacustrine plastisphere: Distinct succession and assembly processes of prokaryotic and eukaryotic communities and role of site, time, and polymer types

Microplastics as a carrier can promote microbial diffusion, potentially influencing the ecological functions of microbial communities in aquatic environments. However, our understanding of the assembly mechanism of microbial communities on different microplastic polymers in freshwater lakes during succession is still insufficient, especially for the eukaryotes. Here, the colonization time, site, and polymer types of microplastics were comprehensively considered to investigate the composition and assembly of prokaryotic and eukaryotic communities and their driving factors during the lacustrine plastisphere formation. Results showed that the particle-associated microorganisms in water were the main source of the plastisphere prokaryotes, while the free-living microorganisms in water mainly accounted for the plastisphere eukaryotes. The response of prokaryotic communities to different microplastic polymers was stronger than eukaryotic communities. The assembly of plastisphere prokaryotic communities was dominated by homogenizing processes (mainly homogenous selection), while the assembly of eukaryotic communities was dominated by differentiating processes (mainly dispersal limitation). Colonization time was an important factor affecting the composition of prokaryotic and eukaryotic communities during the formation of the plastisphere. The Chao1 richness of prokaryotic communities in the plastisphere increased with the increase of colonization time, whereas the opposite was true in eukaryotic communities. This differential response of species diversity and composition of prokaryotic and eukaryotic communities in the plastisphere during dynamic succession could lead to their distinct assembly processes. Overall, the results suggest that distinct assembly of microbial communities in the plastisphere may depend more on specific microbial sub-communities and colonization time than polymer types and colonization site.

Association between primary Sjögren's syndrome and gut microbiota disruption: a systematic review and meta-analysis.

Evidence of gut microbiota disruption for numerous autoimmune diseases has accumulated. Recently, the relationship between the microbiota and primary Sjögren's disease has been increasingly investigated but has yet to be systematically elucidated. Therefore, a meta-analysis of publications dealing on topic was conducted. Case-control studies comparing primary Sjögren's syndrome patients and healthy controls (HCs) were systematically searched in nine databases from inception to March 1, 2023. The primary result quantitatively evaluated in this meta-analysis was the α-diversity. The secondary results qualitatively extracted and analyzed were the β-diversity and relative abundance. In total, 22 case-control studies covering 915 pSS patients and 2103 HCs were examined. The quantitative analysis revealed a slight reduction in α-diversity in pSS patients compared to HCs, with a lower Shannon-Wiener index (SMD = - 0.46, (- 0.68, - 0.25), p < 0.0001, I2 = 71%), Chao1 richness estimator (SMD = - 0.59, (- 0.86, - 0.32), p < 0.0001, I2 = 81%), and ACE index (SMD = - 0.92, (- 1.64, - 0.19), p = 0.01, I2 = 86%). However, the Simpson index (SMD = 0.01, (- 0.43, 0.46) p = 0.95, I2 = 86%) was similar in the two groups. The β-diversity significantly differed between pSS patients and HCs. Variations in the abundance of specific microbes and their metabolites and potential functions contribute to the pSS pathogenesis. Notably, the abundance of the phylum Firmicutes decreased, while that of Proteobacteria increased. SCFA-producing microbes including Ruminococcaceae, Lachnospiraceae, Faecalibacterium, Butyricicoccus, and Eubacterium hallii were depleted. In addition to diversity, the abundances of some specific microbes were related to clinical parameters. According to this systematic review and meta-analysis, gut microbiota dysbiosis, including reduced diversity, was associated with proinflammatory bacterium enrichment and anti-inflammatory bacterium depletion in pSS patients. Further research on the relationship between the gut microbiota and pSS is warranted.

The influences of graphene oxide and nitrification inhibitor on vegetable growths and soil and endophytic bacterial communities: Double-edge sword effects and nitrate risk controls

Crop yield and quality are substantial indicators of evaluating agricultural nitrogen management practices, and the nitrate (NO3−-N) is one of the predominant factors affecting crop quality. The NO3−-N accumulation in vegetable crop affects plant growth and quality and human health. Therefore, it is necessary to stimulate vegetable yield but eliminate excessive NO3−-N in soils and plants with feasible management strategies. Graphene oxide (GO) is a novel carbon nanomaterial that has attracted great attention, but rare research has been conducted to quantify the effects of GO on plant NO3−-N accumulation and microbial communities. This study explored effects of the GO and nitrification inhibitors, dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP), on vegetable yields and NO3−-N contents and bacterial communities in soil-cabbage (Brassica rapa subsp. Chinensis) system. The soil NO3−-N content was significantly reduced with the single GO application. The cabbage NO3−-N content was increased by 60.4 % while the cabbage yield was significantly enhanced by 101.9 % with the single GO application. Meanwhile, the Invsimpson index of soil bacterial community and the ACE and Chao1 richness estimators of endophytic bacterial community were significantly decreased by the GO application. Cabbage NO3−-N content was significantly and negatively correlated with the soil Myxococcota, endophytic bacterial community co-occurrence network edge, cabbage soluble sugar and cabbage proline. The GO application generated double-edged sword effects of positively promoting yield but causing risks of NO3−-N accumulation and quality deterioration. However, these adverse effects could be mitigated by the extra nitrification inhibitor application. The potential ecological risks of GO application to the vegetable quality and endophytic community should be considered.

Distinct composition patterns of bacterial and fungal communities and biogeochemical cycling genes depend on the vegetation type in arid soil

Semi-arid and arid regions account for >40 % of the land area worldwide and provide food resources for the world. Nutrient management by farmer's practices, such as fertilization, improves crop production in semi-arid and arid regions, but this can also affect the composition and function of the soil microbial communities. Therefore, in this research, we have examined the composition of the microbial community and biogeochemical cycling genes in arid soil, subjected to nutrient management by farmer's practices, using high-throughput sequencing and a quantitative-PCR-based chip, Quantitative microbial element cycling (QMEC). Proteobacteria and Acidobacteriota, and Ascomycota dominated the composition of bacterial and fungal communities, respectively. Scrubland soils without nutrient management possessed the lowest Chao1 richness and Shannon diversity of the bacterial community but showed higher average Shannon diversity of the fungal community. Acidobacteriota and Gemmatimonadota, copiotrophic members, were found to have a higher percentage in nutrient-managed soils (cotton, fruit, and vegetables) than the scrubland soils. However, Actinobacteria, autochthonous bacteria, were found to have higher relative abundance in soils from the scrubland than from cotton, fruits, and vegetables. Besides, scrubland soils had a higher relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) to support plant growth in the arid and oligotrophic soils. Vegetable soil microbial communities exhibited a higher potential for biogeochemical cycling than soils used for other vegetation types. In soils from cotton and fruits, the bacterial community was more sensitive to soil properties than the fungal community. Nutrients strongly affected the composition of bacterial and fungal communities in soils from vegetables, while salinity drove the microbial communities in scrubland soils. Our results suggest that vegetation types determined the distinct biodiversity patterns of the microbiota (bacteria and fungi) and associated biogeochemical cycling genes in arid soils.

Effect of plant-soil feedback on soil microbial co-occurrence network depends on the stage of secondary succession

Co-occurrence networks of soil microbial community are used to describe co-occurrence relationships in microbial communities, which can better understand the structure, function, and interaction patterns of microbial communities at different succession stages, but how co-occurrence networks within microbial communities respond to the effects exerted by plants come from different successional stages is unknown. Changes in the co-occurrence network of soil fungal and bacterial communities after plant species grown under monoculture were analyzed with a greenhouse experiment using the rhizosphere soils collected from early-, mid-, and late-successional species in the field. Results showed that compared with the soil microbial communities of plants grew in their own soil conditions, significant changes were observed in the Chao1 and ACE richness of the fungal community and Shannon and Simpson indices of the bacterial community after the growth of plants in other stages of succession; the relative abundance of the bacterial communities were mainly affected rather than the fungal communities at the phylum level. The late-successional species (or mid-successional species) mainly increased the graph density and average clustering coefficient (network complexity) of the fungal and bacterial communities in soil conditioned by the early- and mid-successional species (or early-successional species). Soil water-soluble nitrogen and phosphorus were the main soil factor affecting the relative abundance of the fungal and bacterial communities in species succession. The pre-successional species may be replaced directly by the subsequent plant species in a succession sequence given the network complexity of soil microbial communities.