Operational Taxonomic Units Richness Research Articles

Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and grape quality in vineyards

Abstract Pesticides can have unintentional effects on non‐target organisms and change biotic communities. Such changes might be particularly important in soil microbial communities, which drive many ecosystem functions and may affect crop quality. Here, we investigated, in a three‐year study, how vegetation control (by herbicide application) and soil copper content (from long‐term copper‐based fungicide application) affect biodiversity and the community structure of soil bacteria, fungi and protists, and associated soil functions (respiration, decomposition) in Swiss vineyards. Furthermore, we determined the effects of these two management practices on grape quality as the most direct ecosystem service to farmers. Across all study years, the community composition of microorganisms was affected by herbicide application, however, a significant loss of operational taxonomic units (OTUs) was only observed in fungi and protists. Soil copper content reduced OTU richness of bacteria and protists in some years but had no significant effect on fungal richness. Copper changed the community composition in all three groups of soil microorganisms. While we found no effect of copper on soil functions, herbicide application reduced microbial respiration and biomass by about 39% and 45%, respectively. However, decomposition rates remained virtually unchanged by any pesticide. Yeast assimilable nitrogen (YAN) levels in grape were below the critical threshold of 140 mg/L in 40% of the vineyards without herbicide application and the variety Chasselas, whereas in vineyards with herbicide application, it was only 20%. Application of pesticides led to changes in richness and composition of soil microbial communities and directly reduced some soil functions (microbial biomass and respiration) but not all (decomposition). Some grape quality parameters can be indirectly enhanced by pesticide application, highlighting the trade‐off between the interests of nature conservation and the interests of the farmer. Balancing these two diverging interests requires the establishment of alternative vineyard management allowing reduced pesticide application.

Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts

AbstractEnvironmental DNA (eDNA) extracted from water is routinely used in river biodiversity research, and via metabarcoding eDNA can provide comprehensive taxa lists with little effort and cost. However, eDNA‐based species detection in streams and rivers may be influenced by sampling season and other key factors such as water temperature and discharge. Research linking these factors and also informing on the potential of eDNA metabarcoding to detect shifts in ecological signatures, such as species phenology and functional feeding groups across seasons, is missing. To address this gap, we collected water samples every 2 weeks for 15 months at a long‐term ecological research (LTER) site and at three different positions in the river's cross section, specifically the water surface, riverbed, and riverbank. For these 102 samples, we analyzed macroinvertebrate species and molecular operational taxonomic unit (OTU) richness and temporal community turnover across seasons based on cytochrome c oxidase subunit I (COI) metabarcoding data. Using Generalized Additive Models, we found a significant influence of sampling season on species richness. Community turnover followed a cyclic pattern, reflecting the continuous change of the macroinvertebrate community throughout the year (“seasonal clock”). Although water temperature had no influence on the inferred species richness, higher discharge reduced the number of Annelida and Ephemeroptera species detectable with eDNA. Most macroinvertebrate taxa showed the highest species richness in spring, in particular merolimnic species with univoltine life cycles. Further, we detected an increase in the proportion of shredders in winter and parasites in summer. Our results show the usefulness of highly resolved eDNA metabarcoding time series data for ecological research and biodiversity monitoring in streams and rivers.

The effect of fermented feed (FF) on intestinal, surrounding water, and sediment microbiomes of the Chinese mitten crab Eriocheir sinensis

AbstractObjectiveFermented feed (FF) has several significant advantages in aquaculture. However, little is known about the characteristics of intestinal and environmental microbiota in the Chinese mitten crab Eriocheir sinensis.MethodsThis study was conducted to elucidate the relationship between bacterial communities in the intestine of Chinese mitten crabs and the surrounding environment and to compare the bacterial communities in FF and non‐FF diet modes by using 16S ribosomal RNA high‐throughput sequencing technology.ResultFermented feed diets mainly influenced the alpha diversity of intestinal microbiomes but could affect microbial community structures of beta diversity in water and sediment. Compared to water and sediment, crab intestines had the lowest operational taxonomic unit (OTU) richness and bacterial community diversity. The OTU richness and Chao richness index values were lower in the intestines of crabs that received FF than in crabs that were given non‐FF. No significant differences were observed in the bacterial diversity and OTU richness of water and sediment between the two feeding modes. The bacterial community structures were significantly different among the three environments. Tenericutes, Proteobacteria, and Actinobacteria were the most abundant phyla in the crab intestine, sediment, and water, respectively. Bacterial functions were also different among the three environments. Proportions of nitrate reduction and fermentation in the crab intestine, proportions of nitrification and sulfate respiration in the sediment, and proportions of chemoheterotrophy and aerobic chemoheterotrophy in the water were higher for the FF feeding mode than for the non‐FF mode.ConclusionThe bacterial community structures were significantly different among the three environments. The microbiome of the crab intestine was partially shared with that of the ambient environment. Additionally, the FF mainly influenced the alpha diversity of intestinal microbiomes but also affected the community structures of beta diversity in water and sediment. These results will help us to devise dietary strategies to influence the crab intestinal microbiota and provide guidance for sustainable crab culture practices.

Long-term Consequences on Soil Fungal Community Structure: Monoculture Planting and Natural Regeneration.

Understanding the regeneration and succession of belowground communities, particularly in forests, is vital for maintaining ecosystem health. Despite its importance, there is limited knowledge regarding how fungal communities change over time during ecosystem development, especially under different forest restoration strategies. In this study, we focused on two restoration methods used in northern Japan: monoculture planting and natural regeneration. We examined the responses of the fungal community to monoculture plantations (active tree planting) and naturally regenerated (passive regeneration) forests over a 50-year chronosequence, using natural forests as a reference. Based on DNA metabarcoding, we assessed the richness of fungal Operational Taxonomic Units (OTUs) and their dissimilarity. Our findings revealed that soil fungal richness remained stable after natural regeneration but declined in monoculture plantations, from 354 to 247 OTUs. While the compositional dissimilarity of fungal assemblages between monoculture plantations and natural forests remained consistent regardless of the time since tree planting, it significantly decreased after natural regeneration, suggesting recovery to a state close to the reference level. Notably, the composition of key functional fungal groups-saprotrophic and ectomycorrhizal- has increasingly mirrored that of natural forests over time following passive natural regeneration. In summary, our study suggests that monoculture plantations may not be effective for long-term ecosystem function and service recovery because of their limited support for soil fungal diversity. These results underscore the importance of natural regeneration in forest restoration and management strategies.

Experimental erosion of microbial diversity decreases soil CH4 consumption rates.

Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4 ) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101 -107 -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.

Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system

AbstractIn river systems worldwide, land cover changes have been identified as major drivers of biodiversity change. Quantifying how terrestrial land cover impacts riverine diversity requires local biodiversity assessments. In this study, we investigated the association of terrestrial land cover and the corresponding riverine fish species communities using eDNA‐metabarcoding in the Chinese Shaying River basin. This basin is home to about 37 million people and is largely dominated by a mix of intense agriculture and urban areas, creating a relatively homogeneous, intensely used landscape. We investigated whether the homogeneous landscape is mirrored in the composition and structure of fish communities in the river network. We sampled eDNA in spring and fall of 2018, amplified it with a primer designed for local fish species and used operational taxonomic units (OTU) assigned to fish as proxy for diversity. Furthermore, we used redundancy analysis, general linear models, and distance decay curves to assess the effects of land cover on fish communities. We found that the Shaying River showed relatively high basin‐wide richness (63 OTU) and seasonal differences in local richness, but limited community differentiation. Variations in alpha‐ and beta‐diversity, measured as local OTU richness and pairwise distance‐decay across the basin were low. Redundancy analysis showed only a weak association between observed aquatic communities and their terrestrial surroundings in a 10 km buffer upstream. The lack of community differentiation assessed by eDNA metabarcoding reflects the homogeneous and intense land‐use in this basin.

A mixture of Nordic berries improves cognitive function, metabolic function and alters the gut microbiota in C57Bl/6J male mice.

Our diets greatly influence our health. Multiple lines of research highlight the beneficial properties of eating berries and fruits. In this study, a berry mixture of Nordic berries previously identified as having the potential to improve memory was supplemented to young C57Bl/6J male mice to investigate effects on cognition function, metabolic health, markers of neuroinflammation, and gut microbiota composition. C57Bl/6J male mice at the age of 8 weeks were given standard chow, a high-fat diet (HF, 60%E fat), or a high-fat diet supplemented with freeze-dried powder (20% dwb) of a mixture of Nordic berries and red grape juice (HF + Berry) for 18 weeks (n = 12 animals/diet group). The results show that supplementation with the berry mixture may have beneficial effects on spatial memory, as seen by enhanced performance in the T-maze and Barnes maze compared to the mice receiving the high-fat diet without berries. Additionally, berry intake may aid in counteracting high-fat diet induced weight gain and could influence neuroinflammatory status as suggested by the increased levels of the inflammation modifying IL-10 cytokine in hippocampal extracts from berry supplemented mice. Furthermore, the 4.5-month feeding with diet containing berries resulted in significant changes in cecal microbiota composition. Analysis of cecal bacterial 16S rRNA revealed that the chow group had significantly higher microbial diversity, as measured by the Shannon diversity index and total operational taxonomic unit richness, than the HF group. The HF diet supplemented with berries resulted in a strong trend of higher total OTU richness and significantly increased the relative abundance of Akkermansia muciniphila, which has been linked to protective effects on cognitive decline. In conclusion, the results of this study suggest that intake of a Nordic berry mixture is a valuable strategy for maintaining and improving cognitive function, to be further evaluated in clinical trials.

A cryptically diverse microbial community drives organic matter decomposition in forests

Despite the critical role of microorganisms in plant and fungal residue decomposition, our understanding of their full diversity remains limited. This is due largely to the rapid microbial succession during decomposition, a scarcity of studies including multiple sampling times, and the omission of a species richness index encompassing all decay stages. To address these gaps, we conducted a meta-analysis of 12 studies, each examining bacterial and fungal communities at multiple time points during decomposition. We aimed to determine the overall microbial diversity involved in decomposition processes by aggregating microbial richness at different time points. By comparing cumulative microbial OTU (operational taxonomic unit) richness with single time point microbial richness, we show that the cumulative richness was 2–5 times greater, indicating that a high yet frequently overlooked diversity of microorganisms is involved in the decomposition process. This pattern was consistent across different organic matter types (plant and fungal residues) for both major microbial domains (bacteria and fungi). Moreover, the appearance rate of novel OTUs generally decreased over time for most organic matter types, except for dead wood, which accumulated new fungal OTUs at a notable pace. Our results collectively emphasize the importance of considering various microbial domains, organic matter types, and time points to successfully characterize the diversity of microorganisms involved in decomposition. Further, given the hidden cumulative number of bacterial and fungal species held within plant and fungal residues across decay stages, we propose that these substrates are crucial microbial reservoirs to include to accurately assess global terrestrial microbial diversity.

Diet affects the growth and behavior of Argiope bruennichi spiders and correlates with the species richness of their vertically and horizontally transmitted tissue-resident bacteria

The ability to spread and build quality webs is crucial to spider survival. These abilities may differ in response to dietary adjustments and changes in assemblages of tissue-resident bacteria, including vertically transmitted endosymbiotic taxa, particularly when expanding outside the native ranges. We measured the physical and behavioral parameters of the invasive wasp spider Argiope bruennichi subjected to four types of diets, including protein-rich and lipid-rich diets. We used 16S rDNA sequencing to evaluate vertically and horizontally transmitted tissue-resident bacteria, including endosymbionts, in the cephalothorax and legs of the tested spiders. The diet composition affected the body weight and carapace length as well as the locomotor parameters but not the orb-weaving abilities. Dietary treatments led to changes in the diversity and operational taxonomic unit (OTU) richness of facultative and obligate tissue endosymbionts, with Wolbachia and Rickettsia having higher relative abundance in spiders fed a lipid-rich diet. The higher OTU richness of facultative and obligate endosymbionts was associated with better locomotor performance. The other tissue-resident microbes were dominated by Firmicutes; the dominance and diversity of tissue-resident microbiomes also differed among spiders treated with different diets. The highest alpha diversity of tissue-resident microbes was present in spiders fed the standard diet, whereas all other diets led to a decrease in alpha diversity and various changes at the level of individual genera and OTUs. In conclusion, the tissues of A. bruennichi host tremendously diverse assemblages of bacteria, including obligate or facultative endosymbionts, which are sensitive to differences in diet composition and affect the locomotion of their hosts.

Effects of Cadmium Stress on Bacterial and Fungal Communities in the Whitefly Bemisia tabaci.

Heavy metal contamination is among the most prominent environmental problems in China, posing serious threats to both ecosystem and human health. Among the diverse heavy metal contaminants, cadmium is the most serious. The whitefly Bemisia tabaci is a cosmopolitan pest capable of causing severe damage to a broad range of agricultural crops, especially vegetables. At present, little is known about the effects of cadmium stress on B. tabaci, including on its bacterial and fungal communities. In the current study, we investigated the effects of cadmium on bacterial and fungal communities in whiteflies. Meta-barcode sequencing of the 16S rRNA gene revealed that the whitefly bacterial community contained 264 operational taxonomic units (OTUs) belonging to 201 known genera and 245 known species. The top five most frequent bacterial genera were Rickettsia, Rhodococcus, Candidatus Portiera, Candidatus Hamiltonella, and Achromobacter. Meta-barcode sequencing of the fungal ITS locus revealed that the whitefly fungal community contained 357 OTUs belonging to 187 known genera and 248 known species. The top five most frequent fungal genera were Wallemia, unclassified_f_Dipodascaceae, Apiotrichum, Penicillium, and unclassified_o_Saccharomycetales. Cadmium exposure reduced the fungal OTU richness but increased the bacterial Shannon and Simpson diversity indices in whiteflies. In addition, upon exposure to cadmium, the microbial community composition in whiteflies changed significantly, with increased prevalence of the bacterial genera Rhodococcus and Exiguobacterium and fungal genus Wallemia. Our results indicate that the whitefly microbiota likely contributed to their adaptation and resistance to cadmium and suggested that whiteflies may contain microbes that could help remediate cadmium contamination in natural environments and agricultural fields.

Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.

Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.

Toward non-invasive collection methods for sampling the microbiome of diabetic foot ulcers.

Identifying the microbiome within chronic diabetic foot ulcers is essential if effective antimicrobial therapies are to be administered. Using culture and 16S rRNA gene sequencing, the aim of this study was to compare the microbiome of paired tissue scraping samples with swab samples, collected from participants during attendance at a high-risk foot clinic. The mean richness of cultured swab and tissue scraping samples was consistent, with anaerobes infrequently isolated from both sample types. Comparing percentage frequencies of detection of selected genera of known and potential pathogens namely Staphylococcus, Streptococcus, Enterococcus, Corynebacterium, Enterobacteriaceae and Pseudomonas from cultured and sequenced swab and tissue scrapings indicated that both collection methods captured varying percentages of all the selected genera. The mean abundance of sequenced samples was not significantly different between swabs and tissue scrapings. The mean richness or number of distinct operational taxonomic units (OTUs) and Shannon's H diversity index were not significantly different between the two collection methods. The mean relative abundance of the selected genera of known and potential pathogens, including anaerobes Anaerococcus and Finegoldia, was higher in swabs compared with tissue scrapings and significantly so in Staphylococcus and Pseudomonas genera. Multivariate analyses confirmed no significant differences between the bacterial community compositions of the paired samples. These results suggest that tissue scrapings and swabs can effectively capture the microbiome of chronic DFUs using culture and 16S rRNA gene sequencing.

Effects of grazing prohibition on nirK- and nirS-type denitrifier communities in salt marshes.

Grazing prohibition is an effective management practice to restore salt marsh functioning. However, the effects of grazing exclusion on denitrifying microbial communities and their controlling factors in salt marshes remain unclear. In this study, we surveyed soil physicochemical properties and above- and below-ground biomass and using quantitative polymerase chain reaction and Illumina MiSeq high-throughput sequencing technology to determine the relative abundance, composition, and diversity of nitrite reductase nirS- and nirK-type denitrifying bacterial communities associated with grazing prohibition treatments and elevations. The abundance of nirS-type denitrifiers increased with grazing prohibition time, whereas the abundance of nirK-type denitrifiers remained unaltered. Moreover, nirS-type denitrifiers were more abundant and diverse than nirK-type denitrifiers in all treatments. Grazing prohibition significantly altered the operational taxonomic unit richness, abundance-based coverage estimator, and Chao1 indices of the nirS-type denitrifying bacterial communities, whereas it only minimally affected the structure of the nirK-type denitrifying bacterial community. The results imply that the nirS community, rather than nirK, should be the first candidate for use as an indicator in the process of salt marsh restoration after grazing prohibition. Substances of concern, total nitrogen, and salinity were the key environmental factors affecting the abundance and community composition of nirS and nirK denitrifiers. The findings of this study provide novel insights into the influence of the length of grazing prohibition and elevation on nirS- and nirK-type denitrifying bacterial community composition in salt marshes.

Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.

Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.

Leaf litter arthropods show little response to structural retention in a Central European forest

Decomposition of leaf litter is a central process of energy and nutrient cycling in forests, in which arthropods hold important roles. Thus, safeguarding the diversity of organisms including arthropods is increasingly being considered in contemporary forestry, not least to facilitate continued ecosystem functioning. Retention forestry tries to achieve biodiversity conservation by preservation of tree structural elements such as deadwood and tree microhabitats to provide more heterogeneous habitat. Leaf litter arthropods are, however, only indirectly connected with tree structure, which raises the question if and how the currently practised retention forestry influences the leaf litter arthropod community. As the leaf litter arthropod community includes a very diverse range of taxa that is challenging to identify morphologically, we sampled environmental DNA from leaf litter on 66 plots in the Black Forest in southern Germany that were distributed over gradients of forest and landscape features and differed in forest management intensity. We found that the richness of operational taxonomic units, a surrogate for species, was not related to forest structure but tended to increase with recent harvest intensity (which did not exceed a medium harvest intensity on our plots). Community composition was related to the share of coniferous trees present on a plot, and to a lesser extend to elevation and leaf litter coverage. Our results indicate that the leaf litter arthropod community is not responsive towards different degrees of forest structural changes introduced by management as long as the forest type is retained.

Does helimulching after severe wildfire affect soil fungal diversity and community composition in a Mediterranean ecosystem?

Straw helimulching was applied to an area with a high soil erosion risk one month after the Navalacruz megafire (Iberian Central System, Ávila, Spain) to mitigate soil erosion and to maintain soil quality. To determine whether the soil fungal community, which is key to soil and vegetation recovery after fire, is altered by straw mulching, we examined the effect of helimulching one year after its application. Three hillside zones were chosen with two treatments in each zone (mulched and non-mulched plots), with three replicates of each treatment. Chemical and genomic DNA analyses of soil samples from mulched and non-mulched plots were performed to assess the soil characteristics and the soil fungal community composition and abundance. The total fungal operational taxonomic unit richness and abundance did not differ between treatments. However, there was an increase in the richness of litter saprotrophs, plant pathogens and wood saprotrophs associated with the application of straw mulch. The total fungal composition of mulched and non-mulched plots differed significantly. Fungal composition at the phylum level correlated with the soil potassium content and marginally with the pH and phosphorus content. The application of mulch promoted the dominance of saprotrophic functional groups. Fungal composition according to guilds was also significantly different between treatments. As conclusion, the application of mulch could mean a faster recovery of saprotrophic functional groups that will be responsible for decomposing the available dead fine fuel.

Natural restoration alters soil microbial community structure, but has contrasting effects on the diversity of bacterial and fungal assemblages in salinized grasslands

Natural restoration has often been considered an effective measure for rehabilitating degraded ecosystems. However, its impact on the structure and diversity of soil microbial communities, particularly within a salinized grassland during its restoration succession, remains unclear. In this study, we examined the effects of natural restoration on the Shannon-Wiener diversity index, Operational Taxonomic Units (OTU) richness, and structure of the soil microbial community of a sodic-saline grassland in China using high-throughput amplicon sequencing data from representative successional chronosequences. Our results indicated that natural restoration resulted in a significant mitigation of the grassland salinization (pH from 9.31 to 8.32 and electrical conductivity from 393.33 to 136.67 μs·cm−1) and a significant alteration of the soil microbial community structure of the grassland (p < 0.01). However, the effects of natural recovery differed in terms of the abundance and diversity of bacteria and fungi. For example, the relative abundance of the bacterial phyla Acidobacteria increased by 116.45 % in the topsoil and 339.03 % in the subsoil, while that of the fungal phyla Ascomycota decreased by 8.86 % in the topsoil and 30.18 % in the subsoil. There was no significant effect of restoration on bacterial diversity, but fungal diversity increased by 15.02 % in the Shannon-Wiener index and 62.20 % in the OTU richness in the topsoil. Model-selection analysis further corroborated that the alteration of the soil microbial structure by natural restoration may be due to the fact that the bacteria could adapt to the alleviated salinized grassland soil and the fungi could adapt to the improved soil fertility of the grasslands. Overall, our results contribute to an in-depth understanding of the impacts of natural restoration on soil microbial diversity and community structure in salinized grasslands during the long-term successional course. This may also help to apply natural restoration as a greener practice option for managing degraded ecosystems.

Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field.

Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.

The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats

BackgroundArtificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.ResultsThe results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.ConclusionsThis study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.

Characterization of the oral microbiome and gut microbiome of dental caries and extrinsic black stain in preschool children.

A lower prevalence of dental caries (hereafter termed "caries") has been observed in children with dental extrinsic black stain (EBS). We investigated the epidemiologic characterization of EBS and explored the possible role of the oral microbiome (OM) and gut microbiome (GM) in EBS formation and caries prevention. In an epidemiologic survey, 2,675 children aged 3-6 years were included. Thirty-eight of these children (7 children had both caries and EBS, 10 had EBS only, 11 had caries only, and 10 were healthy children) were recruited for 16S rRNA sequencing and collection of samples of supragingival plaque and feces. Collected plaque samples were divided into four groups: BCP (EBS+, caries+), BP (EBS+, caries-), CP (EBS-, caries+), and P (EBS-, caries-). Fecal samples were also divided into four groups: BCF (EBS+, caries+), BF (EBS+, caries-), CF (EBS-, caries+), and F (EBS-, caries-). EBS was observed in 12.10% of this population. Children with EBS had a significantly reduced prevalence of caries and a lower mean value of decayed-missing-filled teeth (dmft; p < 0.01). According to analyses of dental plaque, the P group had the most complex microbiome. The BCP group exhibited greater operational taxonomic unit (OTU) richness but a reduced evenness compared with the BP group, and the CP group showed greater OTU richness than the BP group. At the genus level, higher abundance of Actinomyces and Cardiobacterium species was observed in the BCP group. Higher abundance of Lautropia and Pesudopropionibacteriumin species was observed in the BP group compared with P and CP groups, respectively (p < 0.05). Veillonella species were significantly more common in P and CP groups than in BP groups, whereas Porphyromonas and Fusobacterium species were more common in the CP group (p < 0.05). With regard to the GM, the CF group exhibited greater OTU diversity than the BF group. The GM in the BCF group exhibited the most complex relationships across all fecal groups. GM groups could be distinguished by various unique biomarkers, such as Escherichia and Shigella species in the BCF group, Agathobacter and Ruminococcus species in the CF group, Lactobacillus species in the BF group, and Roseburia species in the F group. Our results suggest that EBS is a possible protective factor against early-childhood caries. Dental plaque and the GM may be relevant to EBS in primary dentition.