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In order to study the effects of adding different types of rice straw on soil bacterial communities under continuous cropping of flue-cured tobacco, fresh rice straw (FS) and rotted rice straw (RS) were added in soil, with no straw as control (CK). The community composition and diversity of soil bacteria and fungi at different times (0, 7, 30, 60 and 90 d) under 3 treatments were studied by high-throughput sequencing. The results showed that fresh rice straw and rotted rice straw could significantly improve the diversity and richness of soil microbial community. After 90 d in FS and RS treatments, the Chao 1 index, Shannon index and Simpson index of bacteria and the Chao 1 index of fungi were significantly improved. The analysis of community structure composition showed that FS and RS treatments increased the relative abundances of Proteobacteria, Spirochaetes and Verrucomicrobia. FS treatment increased the relative abundance of Basidiomycota, and decreased the relative abundances of Chytridiomycota and Rozellomycota. RS treatment increased the relative abundances of Ascomycota and Basidiomycota, and decreased the relative abundances of Zygomycota and Chytridiomycota. In summary, the addition of fresh rice straw and rotted rice straw could change the community composition of soil bacteria and fungi, improve the health status of soil with continuous cropping of flue-cured tobacco. Compared with rotted rice straw treatment, fresh rice straw treatment increased the abundance of pathogenic fungi. [ABSTRACT FROM AUTHOR]

In this study, the phytoremediation potential of Taro (Colocasia esculenta L. Schott) plant was examined, utilizing horizontal subsurface flow constructed wetlands with and without an electric current supply for the purpose of removing pollutants from paper mill effluent. For this, different wetlands were set up with varying concentrations of effluent: CW (Control), CW1 (25%), CW2 (50%), CW3 (75%), CW4 (100%). After 45 days, the highest plant height (85.13 ± 4.24 cm), leaf area index(250.83 ± 10.14), fresh biomass (565.30 ± 6.10 g), root biomass (392.85 ± 4.34 g), root-to-shoot ratio (2.41 ± 2.10), relative growth rate (0.044 ± 0.002 gg−1d−1), and chlorophyll content (3.29 ± 0.07 mg/g fwt) was observed in CW2 with current supply, along with significant removal of pollutants (pH: 7.13 ± 0.15, EC: 2.33 ± 0.07 dS/m, TDS: 192.52 ± 6.12 mg/L, COD: 490.17 ± 5.01 mg/L, BOD: 206.74 ± 5.92 mg/L, potassium: 73.27 ± 4.11 mg/L, sodium: 46.62 ± 2.27 mg/L, phosphate phosphorus: 34.08 ± 1.43 mg/L, and nitrate nitrogen: 104.85 ± 5.94 mg/L) and highest first-order rate constant (k) values. Furthermore, the microbial community assessment of constructed wetlands using V3-V4 16S rRNA sequence data was prepared on the Illumina MiSeq framework. The major phyla identified were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Chloroflexi, Acidobacteria, Nitrospirae, Planctomycetes, and others. The findings offer innovative insights for sustainable wastewater treatment strategies through phytoremediation of paper mill effluent using Taro plants in modified constructed wetlands and highlight the role of diverse microbial communities capable of degrading various pollutants in wastewater. [ABSTRACT FROM AUTHOR]

Abstract Background Fish gut microbiota undergo dynamic changes under the influence of many factors and play an important role in the nutrition, immunity and development in fish. Although common carp (Cyprinus carpio L.) is an economically important freshwater fish, there are few reports on its gut microbiota changes at different early developmental stages. In the present study, the gut microbiota of common carp during the early developmental stages and its correlation with the feed and pond water flora were studied using the Illumina MiSeq sequencing platform. Results The results showed that the gut microbiota of common carp underwent continuous and mild changes over the development process, and the pond water environment might provide bacterial resources and have a certain influence on the changes in the gut microbiota of common carp. However, host selection pressure played a more important role in shaping the gut microbiota. Although the gut microbiota was affected by many factors, the presence of core microbiota indicated that some bacterial species adapt to the gut microenvironment of common carp and played a role in its growth process. Conclusions The dynamic changes of gut microbiota of carp in early development stage were related to the feed, water environment and host selection. The results of this study provide a theoretical basis for healthy farming and disease prevention of common carp.

Helan Mountain is located in the arid and semi-arid region of northwest China. Systematic analysis of the composition characteristics of soil fungal communities in this area is of great significance for clarifying the fungal diversity and community functions in forest ecosystems of arid and semi-arid regions. The Illumina Miseq high-throughput sequencing technology was used to analyze the fungal diversity, community composition, and their responses to changes of soil physicochemical properties in three main constructive tree species—Picea crassifolia, Pinus tabuliformis and Betula platyphylla in Helan Mountain. The results revealed that a total of 276, 353 and 433 fungal OTUs were obtained from rhizosphere soil with 60 shared OTUs. All fungal OTUs belonged to 17 phyla, 42 classes, 107 orders, 210 families and 326 genera. At the phylum level, Basidiomycota and Ascomycota were dominant, with relative abundances of 58. 7% and 35. 7%, respectively. At the genus level, the top five dominant genera were Sebacina(6. 7%), Tomentela (6. 5%), Inocybe(6. 1%), Geminibasidium(3. 7%) and Penicillium(2. 9%). Significant differences were observed in the composition of dominant fungi community at the genus level among different tree species. The genera with the highest relative abundance in the rhizosphere soil are Geminibasidium(10. 8%), Inocybe(16. 9%), and Sebacina(9. 0%) respectively. RDA was used to analysis the driving factors of fungal community composition difference in the rhizosphere soil of the main constructive tree species in Helan Mountain. Soil total nitrogen content (TN) and soil water content (SWC) exert significant influences on the composition of fungal communities, accounting for explanation of 41. 6% and 39. 1%, respectively. This study enriches the biological information of fungal resources in the rhizosphere soil of the main tree species in Helan Mountain, and can provide theoretical basis for the excavation and research of fungal resources in forest ecosystems in arid and semi-arid areas. [ABSTRACT FROM AUTHOR]

Background: Fish gut microbiota undergo dynamic changes under the influence of many factors and play an important role in the nutrition, immunity and development in fish. Although common carp (Cyprinus carpio L.) is an economically important freshwater fish, there are few reports on its gut microbiota changes at different early developmental stages. In the present study, the gut microbiota of common carp during the early developmental stages and its correlation with the feed and pond water flora were studied using the Illumina MiSeq sequencing platform. Results: The results showed that the gut microbiota of common carp underwent continuous and mild changes over the development process, and the pond water environment might provide bacterial resources and have a certain influence on the changes in the gut microbiota of common carp. However, host selection pressure played a more important role in shaping the gut microbiota. Although the gut microbiota was affected by many factors, the presence of core microbiota indicated that some bacterial species adapt to the gut microenvironment of common carp and played a role in its growth process. Conclusions: The dynamic changes of gut microbiota of carp in early development stage were related to the feed, water environment and host selection. The results of this study provide a theoretical basis for healthy farming and disease prevention of common carp. [ABSTRACT FROM AUTHOR]

Intercropping is widely utilised in agricultural production to enhance land use efficiency because of its benefits, such as heightened crop productivity and optimised resource utilisation. We investigated the effects of Pinto peanut/sisal (HST), Stylo/sisal (strT) and Grona styracifolia/sisal (JqT) intercropping systems on soil bacterial communities compared with sisal continuous cropping (CK) by using Illumina MiSeq high-throughput sequencing technology. The intercropping system significantly increased the total nitrogen (TN), soil pH and soil moisture levels and decreased the levels of available phosphorus (AP) and available potassium (AK). Minimal variations were observed in Shannon's and Simpson's diversity indices between the monoculture and intercropping systems as well as among different intercropping systems. The most abundant phyla observed within the four groups were Proteobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes. At the phylum level, the relative abundances of Proteobacteria, Acidobacteria, Cyanobacteria and Bacteroidetes were 37.37–54.35%, 10.54–21.21%, 3.46–20.43% and 2.15–5.67%, respectively. Compared with ZCK, StrT, JqT and HST treatments led to higher abundance of Cyanobacteria (from 3.46% to 20.43%, 11.37% and 16.58%, respectively) and Bacteroidetes (from 2.15% to 5.67%, 5.21% and 5.10%, respectively). The results of the linear discriminant analysis of effect sizes demonstrated notable variations in the relative abundance of bacterial taxa among various intercropping systems. The dominant categories of the genus in strT and JqT groups were Blastocatellia and Blastocatellaceae-Subgroup4, while Firmicutes was the dominant category of the genus in the HST group. The structure of bacterial communities did not vary between intercropping and monoculture systems. The findings indicated that the impact of the intercropping system on the bacterial community structure was not contingent on the specific intercropping patterns employed. [ABSTRACT FROM AUTHOR]

Most human rotaviruses belong to the Wa-like, DS-1-like, or AU-1-like genotype constellation. The AU-1-like constellation, albeit minor, captured attention because its prototype strain AU-1 originated from feline rotavirus, leading to the concept of interspecies transmission of rotavirus. The AU-1 genome sequence determined by various laboratories over the years has documented two conflicting VP7 sequences in the GenBank. As culture-adaptation may introduce changes in the viral genome, the original fecal (wild-type) and the seed stock of culture-adapted AU-1 genomes were sequenced using the Illumina's MiSeq platform to determine the authentic AU-1 sequence and to identify what mutational changes were selected during cell-culture adaptation. The wild-type and culture-adapted AU-1 genomes were identical except for one VP4-P475L substitution. Their VP7 gene was 99.9% identical to the previously reported AU-1 VP7 under accession number AB792641 but only 92.5% to that under accession number D86271. Thus, the wild-type sequences determined in this study (accession numbers OR727616-OR727626) should be used as the reference. The VP4-P475L mutation was more likely incidental than inevitable during cell-culture adaptation. This was the first study in which the whole genomes of both wild-type and cultured RVA strains were simultaneously determined by deep sequencing. [ABSTRACT FROM AUTHOR]

Daqu is a typical multi-enzyme and multi-microbes fermentation starter of traditional Chinese liquor. The culture-independent molecular method has become a general method for the study of the Daqu microbial community. To determine the most suitable DNA extraction method of Daqu samples, the effects of different DNA extraction methods on Daqu genomic DNA extraction and amplicon libraries were evaluated. In this study, four DNA extraction methods were selected for the extraction of microbial DNA from two kinds of Daqu. Combined with DNA extraction quality, qPCR quantitative results, Illumina Miseq sequencing results of bacterial 16S rRNA gene, and fungal ITS gene amplicon library, the effects of different extraction methods of Daqu genomic DNA were evaluated. The comprehensive analysis of DNA yield and microbial biomass showed that the DNA yield of the SDS-based extraction method was higher than that of the kit extraction method, and the DNA yield of the in-situ SDS-based extraction method was as high as 5.46 x 104 ng/g, but the DNA purity was low. The qPCR quantitative results of the SDS-based extraction method were 101 - 6 orders of magnitude higher than those of the kit extraction method, and the microbial biomass of the washing-pretreatment plus SDS-based extraction method was the highest, which was 101-3 orders of magnitude higher than that of the in-situ SDS-based extraction method. Whereas the microbial biomass of the DNA extraction kit was the lowest, with only 102-4of the Shannon diversity index among amplicon libraries showed that different DNA extraction methods had significant differences among fungal ITS amplicon libraries, but no significant differences among bacterial 16S rDNA amplicon libraries. The Shannon index of the fungal amplicon library of the washing-pretreated samples were higher than that of the in-situ treated samples. By comparing the operational taxonomic units (OTU) with significant differences among the amplicon libraries, it could be seen that most of the OTUs in the bacterial 16S rDNA amplicon library had differences in abundance, but most of them could be detected in different DNA extraction methods. However, among the fungal ITS amplicon libraries, most OTUs showed a similar trend between different DNA extraction methods, indicating that the DNA extraction method had a significant effect on the extraction of some fungal microbial genomes, and the washing-pretreatment was beneficial to the extraction of fungal genomic DNA. Compared with the four DNA extraction methods, the washing-pretreatment plus SDS-based extraction method was the most suitable for the quantitative and community structure analysis of Daqu microorganisms. [ABSTRACT FROM AUTHOR]

Elucidating the plant−microbiome network is of importance in understanding species coexistence in natural ecosystems. The phyllosphere, which is the aerial parts of terrestrial plants, is inhabited by diverse microbes. However, few studies have focused on the phyllosphere microbiome and plant-microbiome network in temperate grasslands. In this study, we explored the diversity, community structure, and network architecture of phyllosphere bacteria and fungi in 19 plant species native to the temperate grassland in Inner Mongolia, China. We obtained 3,313 and 758 phyllosphere bacterial and fungal operational taxonomic units, respectively, and found that the bacterial community was dominated by Proteobacteria, Actinobacteriota, and Firmicutes, whereas the fungal community was dominated by Ascomycota and Basidiomycota. Plant identity exerted significant impacts on α-diversities of both bacterial and fungal communities. The composition of bacterial and fungal communities differed among plant species. Plant identity had a greater effect on fungal than bacterial communities. Both bacterial and fungal network structures were characterized by specialized, modular, lowly connected, and no nested properties. The plant−fungal network had a high level of specification, modularity, antinestedness, and connectance compared with the plant−bacterial network. Our results suggest more intimate relationships between plants and phyllosphere fungi than between plants and phyllosphere bacteria and also that the phyllosphere fungal community in the temperate grassland ecosystem is more resistant to environmental disturbance than the phyllosphere bacterial community. These findings may contribute to our understanding of the mechanisms by which species coexist and communities stabilize in grassland ecosystems.

Non-chemical methods, including mechanical and manual weed management are important for improving crop yields and preserving soil microbial diversity. In Tunisia, chickpea cultivation uses a combination of these methods to suppress weeds. This study aimed to evaluate the impact of weeding practices on chickpea ( Cicer arietinum L. cultivar REBHA) yield and soil microbial diversity. Field experiments were conducted at the Technical Center for Biological Agriculture in Essaida, Tunisia, using six plots with manual and no weeding treatments. Chickpea yield was measured, and soil samples were collected for metagenomic analysis. Floristic surveys identified 13 weed species, with Chenopodium album L., Rumex acetosa L., and Urtica dioica L. being the most dominant. Seed yield ranged from 23.2 to 26.2 qls/ha in non-weeded plots and from 25.1 to 30.1 qls/ha in weeded plots, showing an increase in yield (11.75%) with manual weeding. Soil metagenomics revealed changes in bacterial community composition between the two treatments. The dominant phylum was Pseudomonadota , whose relative abundance increased from 24.88% in non-weeded plots to 34.76% in weeded plots. Alpha diversity indices showed lower species richness and diversity in weeded soils, with 62000 OTUs in weeded plots compared to 43202 OTUs in non-weeded plots. Betaproteobacteria and Alphaproteobacteria exhibited higher OTU counts in weeded soils. The Simpson diversity index was lower in non-weeded soils (0.025) than in weeded soils (0.075), indicating a more irregular microbial distribution in non-weeded plots. Thus, manual weeding improved chickpea yield and altered the soil bacterial community, increasing diversity in key microbial taxa. This study highlights the complex interaction between weed management practices and soil microbial ecosystems, which may influence crop productivity.

Maize/peanut intercropping may improve soil health through reducing nitrogen (N) fertilization. However, the effects of maize/peanut intercropping combined with reduced N fertilization on the soil fungal community structure have not been well reported. Using a long-term localized micro-zone experiment, we investigated the combined effects of intercropping and N fertilizer application on soil fungal community diversity and composition. Three cropping patterns (maize/peanut intercropping, maize monoculture, and peanut monoculture) and three N application levels (0 kg·hm−2, 150 kg·hm−2, and 300 kg·hm−2) were assessed. The results showed that the total numbers of fungal species and unique species (operational taxonomic units, OTUs) in both maize and peanut soils tended to first increase and then decrease with increasing N application. Compared with monoculture, the numbers of total OTUs and unique OTUs in intercropped maize soil decreased by 4.14% and 12.79%, respectively, but the total numbers of OTUs and unique OTUs in peanut soil increased by 1.08% and 3.78%, respectively. With increasing N application, the soil fungal Ace and Chao indices of maize soil first increased and then decreased, while the fungal Shannon, Ace, and Chao indices of peanut soil decreased. Compared with the monoculture system, intercropping significantly reduced the maize soil fungal Ace and Chao indices but increased the peanut soil fungal Shannon, Ace, and Chao indices. Nitrogen application and intercropping significantly altered the fungal community structure of maize soil, while N application had no significant effect on the fungal community structure of peanut soil, though intercropping significantly changed the fungal community structure of peanut soil. At the phylum level, Ascomycota, Basidiomycota, Mortierellomycota, unclassified_k_Fungi, and Chytridiomycota were the dominant taxa. Redundancy analysis (RDA) showed that soil nitrate (NO3−) content was the main environmental factor shaping the soil fungal community. In conclusion, excessive N fertilization (300 kg·hm−2) can reduce soil fungal community diversity; maize/peanut intercropping reversed the negative effect of N application on fungal community of peanut soil, but not that of maize soil. Soil NO3− content is the primary environmental driver of soil fungal communities. [ABSTRACT FROM AUTHOR]

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[Objective] The study aimed to reveal the microbial community structure and soil physicochemical properties of apple rhizosphere under the intercropping system of persimmon and apple trees. [Method] In the study, rhizosphere soil of intercropping (I) and non-intercropping (NI) apples were used as materials to analyze the rhizosphere microbial community structure by high-throughput sequencing technology. [Result] lnter-cropping of persimmon significautly increased the contents of organic matter (OM), available nitrogen (AN), total phosphorus (TP), decreased the contents of available potassium (AK) in apple rhizosphere soil. The Alpha diversity analysis showed that intercropping had no significant effect on the bacterial richness index and diversity index of apple rhizosphere soil, whereas significantly reduced the Ace index of rhizosphere soil fungi (P = 0. 03). β diversity analysis showed that there were significant differences in bacterial and fungal community structure between intercropped and non-intercropped soils. Further LEfSe analysis showed that intercropping significantly increased the abundance of 17 bacterial genera in apple rhizosphere soil, of which, 9 were known genera, and 8 were unknown genera. These nine known genera included Sporacetigenium, Tepidisphaera, Agromyces, Alkanindiges, Phycisphaera, Pseudoxanthomonas, Terrimonas, Pseudohaliea, Paenisporosarcina; The abundances of four bacterial genera, namely Sporichthya, Methylocystis, Devosia and Alter-erythrobacter were significantly decreased. Intercropping significantly increased the abundance of 1 fungal genus Arthrographis and decreased the abundance of 3 fungal genera, namely Cylindrocarpon, Metacordyceps and Exophiala. Spearman's correlation analysis showed that Pseudomonas was positively correlated with available phosphorus (AP) and TP, while Naganishia was positively correlated with AP. The fungal genera Polyscytalum and Minimedusa showed a significant negative correlation with AP. PICRUSt2 functional prediction analysis showed that intercropping significantly decreased the abundance of carbohydrate transport and metabolism, and extracellular structure in rhizosphere bacteria. FUNGuild analysis showed that intercropping significantly reduced the abundance of pathogen-saprophytic transitional fungi in apple rhizosphere soil. [Conclusion] Intercropping of apple and persimmon trees can increase the contents of OM, AN, TP in apple rhizosphere soil, significantly increase the relative abundance of beneficial rhizosphere microorganisms, and reduce the relative abundance of pathogenic fungi microorganisms, which will provide data reference for exploring the mechanism of intercropping disease resistance. [ABSTRACT FROM AUTHOR]

Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors. The assessment was conducted using Illumina MiSeq sequencing in various altitude gradients and on slopes with different aspects (shady slopes and sunny slopes) in the subalpine meadow of Dongling Mountain, Beijing. Topographical factors had a significant effect on soil physicochemical properties: the primary factors determining the structure of microbial communities are total potassium (TK), ammonium nitrogen (NH4+-N), and soil organic carbon (SOC). There was no significant change in the diversity of the bacterial community, whereas the diversity of the fungal community displayed a single-peaked trend. The effect of slope orientation on microbial communities was not as significant as the effect of elevation on them. The number of bacterial communities with significant differences showed a unimodal trend, while the number of fungal communities showed a decreasing trend. The co-occurrence network of fungal communities exhibits greater intricacy than that of bacterial communities, and bacterial communities are more complex in soils with sunny slopes compared to soils with shady slopes, and the opposite is true for fungal communities. The identification of the main factors that control soil microbial diversity and composition in this study, provided the groundwork for investigating the soil microbial response and adaptation to environmental changes in subalpine meadows. [ABSTRACT FROM AUTHOR]

We deal with various strains of Lactobacillus that can maintain the intestinal microbiome of rats treated with cyclophosphamide, an anticancer agent (chemotherapy). We use MiSeq and various types of statistical tests to prove that cyclophosphamide in rats alters the intestinal microbiome, favoring the growth of various fungi that are extremely harmful to intestinal metabolism. On the contrary, when Lactobacillus 3L is administered together with cyclophosphamide, we prove that the microbiome is preserved by having a much better intestinal metabolism.

The rhizosphere of grown tea (Camellia sinensis (L.) O. Kuntze) becomes acidic, and aluminium (Al) toxicity has been identified as a key constraint on plant development in acidic soils. The current study investigated the composition and functions of rhizosphere bacteria as well as soil enzyme activity under different Al stress conditions. The effect of soil pH, soil enzyme activities, the diversity and structure of the rhizosphere bacterial population under various Al concentrations were studied by the pot experiment. All analyses demonstrated that substantial alterations in the activity of soil enzymes and the composition of the bacterial communities in the rhizosphere could only be seen under conditions of extreme Al stress. Soil enzymes were more concentrated in Al concentrations of 100, 150 and 250 µM, respectively. More than 82,000 valid reads were obtained for each replicate, and the abundance of certain genera in the aluminium treated groups were greater than the control group. Lower Al stress attracted Al-tolerant bacteria such as Burkholderia to increase Al stress resistance. These findings revealed that soil enzyme activities and the structure of the rhizosphere bacterial population in tea orchard soil provided tolerance or resistance capability to tea plants for their development under Al stress.

Oases soils in northwestern China are used widely for agricultural production, but low soil moisture and fertility necessitate high volumes of irrigation and fertilization, with significant losses of water via evaporation and nitrogen via denitrification. The dynamics of denitrifying communities and their responses to potential denitrification rate (PDR) in continuously irrigated oases remain unclear. In this study, we examined the dynamics of nirK and nirS denitrifying communities in three distinct areas, an old oasis field (OOF, 54 years of cultivation), a young oasis field (YOF, 20 years) and an adjacent uncultivated sandy land (USL, 0 years), and used the partial least squares path model (PLS‐PM) to predict how and to what extent soil properties and denitrifying communities may be responsible for changes in PDR. Our findings indicate that cultivation, compared with the USL treatment, improved soil structure and fertility and increased the abundance and diversity of denitrifying microbes, resulting in a further elevation of soil PDR in YOF and OOF. Additionally, our analysis highlights the potential dominance of the nirK gene in denitrification. PLS‐PM revealed that soil chemical properties and microbial biomass indirectly affected soil PDR by regulating the abundance and diversity of nirK and nirS genes. Conversely, soil physical properties had a direct negative impact on PDR. Alterations in PDR were, in part, attributed to changes in abundance, richness and beta‐diversity, but not correlated with changes in alpha‐diversity. Notably, the standardized total effect demonstrated that the denitrifier community exhibited greater responsiveness to changes in PDR than did soil properties. Overall, our findings suggest that denitrifying communities may play a more important role than soil properties in PDR, and an increased understanding of denitrifying communities allows PDR prediction during conversion of oasis to cultivated land. [ABSTRACT FROM AUTHOR]

Shaoxing rice wine is a notable exemplar of Chinese rice wine. Its superior quality is strongly correlated with the indigenous natural environment. The results indicated that Firmicutes (75%), Actinobacteria (15%), Proteobacteria (5%), and Bacteroidetes (3%) comprised the prevailing bacterial groups. Among the main bacterial genera, Lactobacillus was the most abundant, accounting for 49.4%, followed by Lactococcus (11.9%), Saccharopolyspora (13.1%), Leuconostoc (4.1%), and Thermoactinomyces (1.1%). The dominant fungal phyla were Ascomycota and Zygomycota. Among the dominant genera, Saccharomyces (59.3%) prevailed as the most abundant, followed by Saccharomycopsis (10.7%), Aspergillus (7.1%), Thermomyces (6.2%), Rhizopus (4.9%), Rhizomucor (2.2%), and Mucor (1.3%). The findings demonstrate that the structure of the bacterial and fungal communities remains stable in the environment, with their diversity strongly influenced by climatic conditions. The continuous fluctuations in environmental factors, such as temperature, air pressure, humidity, rainfall, and light, significantly impact the composition and diversity of microbial populations, particularly the dominant bacterial community. [ABSTRACT FROM AUTHOR]

The denitrification process is one of the important processes in the soil nitrogen (N) cycle, and is closely related to the loss of soil N fertilizer. Five treatments were included in this study: N0 (control, no N application); N90 (N application rate 90 kg ha−1); N150 (N application rate 150 kg ha−1); N210 (N application rate 210 kg ha−1); and N270 (N application rate 270 kg ha−1), to study the effect of different N application rates on the soil nirS-type denitrifying bacterial community structure, the influence of key enzyme activities during the denitrification process, and the main environmental factors affecting the variation of the denitrifying bacterial community in maize field soil under the mulched fertigation system in the semi-arid region of Northeast China. The results showed that increasing N fertilizer application significantly increased the contents of soil inorganic N and acid-hydrolyzable organic N, but significantly decreased pH. N fertilizer significantly increased nitrate reductase (NAR) activity and nitrite reductase (NIR) activity. Excessive application of N fertilizer significantly increased the nirS gene copy numbers, and, at the same time, significantly decreased the diversity of nirS-type soil denitrifying bacteria. Proteobacteria was the dominant denitrifying phylum in all treatments, and N application promoted the growth of Bradyrhizobium belonging to this phylum. The application of N fertilizer significantly changed the community structure of nirS denitrifying bacteria, and the NO3−-N content was the most important factor for this observation. Soil organic matter (SOM) and non-hydrolyzable N (NHN) indirectly affected the denitrifying bacterial community structure through NAR activity and NIR activity, while soil total N (TN) and nitrate N (NO3−-N) indirectly affected yield through denitrifying bacterial community structure. Although increasing N fertilizer was beneficial in increasing soil nutrients, the community structure of nirS-type denitrifying bacteria changed significantly. This is attributed to the increase in soil NO3−-N accumulation caused by a large amount of N application. The results of this research provide an important scientific basis for further research on the response mechanism of farmland soil denitrifying microorganisms to different N fertilizer managements under the mulched fertigation system in the semi-arid region of Northeast China. [ABSTRACT FROM AUTHOR]

We deal with various strains of Lactobacillus that can maintain the intestinal microbiome of rats treated with cyclophosphamide, an anticancer agent (chemotherapy). We use MiSeq and various types of statistical tests to prove that cyclophosphamide in rats alters the intestinal microbiome, favoring the growth of various fungi that are extremely harmful to intestinal metabolism. On the contrary, when Lactobacillus 3L is administered together with cyclophosphamide, we prove that the microbiome is preserved by having a much better intestinal metabolism. [ABSTRACT FROM AUTHOR]

Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.

Glandora prostrata (Loisel.) D.C.Thomas (Thomas et al., ), besides being a common plant of western and south-western Europe and north-western Africa, is a species with a wealth of reported uses in traditional and folk medicine. The chloroplast genome of Glandora prostrata subsp. lusitanica (Samp.) D.C.Thomas (Thomas et al., ) isolate BPTPS049 described in this study is the first publicly available complete plastome belonging to the Glandora genus. The chloroplast genome (GenBank accession number: ON641304) is 150,041 bp in length with 37.5% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,833 bp each), separated by a large (81,222 bp) and small (17,153 bp) single-copy regions. It has 131 annotated genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis performed confirms that G. prostrata subsp. lusitanica is placed under the Boraginaceae family, which belongs to the Boraginales order. This study will contribute to conservation, phylogenetic, and evolutionary studies that comprise this traditional species relevant to the landscape of aromatic, medicinal, and condiment plants from Portugal.

Despite having many historically reported ethnomedicinal uses, Centaurium erythraea Rafn (Rafn and Buchs, 1800; common centaury) also produces cytotoxic secondary metabolites, and its presence should be carefully monitored. In this study, the complete chloroplast of Centaurium erythraea subsp. majus (Hoffmanns. & Link) M.Laínz (Laínz, 1971) isolate BPTPS121 is described, being the first available plastome belonging to the Centaurium genus. The chloroplast genome (GenBank accession number: ON641347) is 153,107 bp in length with 37.9% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,166 bp each), separated by a large single-copy (84,388 bp) and small single-copy (18,387 bp) regions. A total of 129 genes were predicted, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes. The phylogenetic analysis showed that isolate BPTPS121 is placed under the Gentianaceae family, belonging to the Gentianales order. The maximum-likelihood tree supports the already described lineage divergence in the Gentianaceae family, with C. erythraea subsp. majus belonging to the Chironieae tribe positioned below the Exaceae tribe and above the Potalieae and the entire Gentianeae tribes. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food, feed, and supplements safety purposes.

Atribacteria play an important role in global carbon cycling. Little is known, however, about the Atribacteria communities found in alpine lakes. The presence and diversity of Atribacteria in the sediment core of alpine Sayram lake in China were investigated using Illumina MiSeq sequencing in this study. According to the findings, Atribacteria affiliated with JS1 were dominant in the sediment core of Sayram Lake, with a relative abundance of 0.19 to 10% (average 3.75%) of all bacterial sequences. Furthermore, the relative abundance of Atribacteria associated with JS1 increased with sediment depth. As a result, this study significantly contributes to our understanding of Atribacteria community habitat.

Summary: Fish spoilage is significantly influenced by the microbiota composition, in which the specific spoilage organisms are the main factors. In this article, we used the 16S rRNA V3–V4 hypervariable areas of bacteria to assess the microbial community and metabolic function of Scomber japonicus during storage at 4 °C for 9 days. The physicochemical and microbiological indices including total viable counts (TVC), total volatile basic nitrogen (TVB‐N) and biogenic amines (BAs) were determined. Observations revealed that TVC, TVB‐N and BAs content dramatically increased over the storage, TVB‐N, histamine, cadaverine and tyramine content reached 54.18 mg/100 g, 621.26, 190.93 and 57.48 mg kg−1, respectively, at the end of storage. The decrease of alpha diversity indicated the decrease of microbial community plenty and diversity. Pseudomonas, Acinetobacter and Moraxellaceae unclassified occupied the dominant position during storage. The accumulation of histamine and cadaverine correlated positively with Pseudomonas and Brochothrix while negatively with Acinetobacter, Arthrobacter and Flavobacterium. Putrescine production and Photobacterium showed a strong favourable association. Amino acid metabolism and glucose metabolism were the two primary metabolic routes during the storage of S. japonicus, according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). Overall, this study explored the interrelationships among the microbial community, functional metabolisms and spoilage characteristics during the storage of S. japonicus, which aimed to identify the specific spoilage organisms and help to deepen the understanding of roles that this microbiota played during spoilage. [ABSTRACT FROM AUTHOR]

Pile-fermentation is a common processing step for Phyllanthus emblica L. fruit (PEF) in its producing area. This process enhances its flavor, reduces astringency, and increases its health benefits. However, the mechanism behind pile-fermentation and the key factors impacting PEF quality remain unknown, becoming an urgent challenge that limits its further application. To address this issue, 87 volatile compounds were analyzed by HS-SPME/GC-QQQ-MS/MS and identified acetic acid and ethyl acetate as distinguishing markers before and after fermentation. The results found that 2-methoxy-3-isobutylpyrazine contributes to the differences in odor after fermentation based on the odor intensity characteristic spectrum. Illumina Miseq sequencing of ITS1 region and 16SrDNA V4 region was performed to investigate the microbial succession during the pile-fermentation. A total of 4 phyla 34 genera of fungi and 15 phyla 61 genera of bacteria were detected in all samples. The results showed that the dominant bacteria had significant differences due to different habitats before fermentation, and the diversity increased after fermentation, while the fungal diversity exhibited the opposite trend. Aspergillus and the Unclassified_f_Necriaceae genus emerged as dominant genera after fermentation. Additionally, through UPLC-QTOF-MS analysis, we identified 18 differential components before and after fermentation. Among these, 5 compounds, such as 2-O-galloyl-1,4-galactolactone and 1-methyl-2-gallate galactose ester, showed a downward trend, whereas 13 compounds, including corilagin and chebulitic acid, exhibited an upward trend. These changes weakened astringency while improving sourness and aftertaste sweetness. The results of this study hold significant importance in clarifying the fermentation mechanism and improving the quality standards of PEF.

There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect lowabundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common. [ABSTRACT FROM AUTHOR]

Purpose: Sorbitol and mannitol have profound effects on plant growth, involving plant photosynthesis, respiration and developmental processes, and are also associated with plant health as rhizosphere exudates. However, studies on soil microbial activity and the quality of sugar alcohols as carbon source additives, especially amendments with sorbitol and mannitol, are rarely studied. Materials and methods: Soil nutrients, enzyme activities and microbial communities were measured at 0.25, 0.5 and 1.0 mg sorbitol or mannitol per gram (fresh weight) soil (i.e. mass ratio of sugar alcohol to fresh soil). Results: Increasing soil concentrations of the sugar alcohols led to significantly increased soil concentrations of available potassium and NO3−-N, reduced soil pH and enhanced soil enzyme activities. Soil nutrient levels were enhanced by the sugar alcohols, despite decreasing NO3−-N and available P contents, relative to the control, with mannitol having a greater effect than sorbitol at the same concentration. These two sugar alcohols altered the composition of the soil microbial communities, significantly increasing the soil bacterial communities involved in nitrogen fixation and ureolysis, as well as the proportions of Pseudomonadaceae and Verrucomicrobiaceae which were significantly positively correlated with a variety of enzymes in the soil, particularly invertases. In addition, Xanthomonadaceae, Sphingomonadaceae and Blastocatellaceae were significantly positively correlated with the soil NO3−-N concentration. Conclusions: Sorbitol and mannitol improved soil nutrient environment, accelerated soil nutrient cycling and had screening and improvement effects on soil microbial communities, while mannitol had greater potential than sorbitol. [ABSTRACT FROM AUTHOR]

Soil freeze–thaw processes lead to high nitrous oxide (N2O) emissions and exacerbate the greenhouse effect. The wetlands of the Inner Mongolia Plateau are in the pronounced seasonal freeze–thaw zone, but the effect of spring thaw on N2O emissions and related microbial mechanisms is still unclear. We investigated the effects of different periods (freeze, freeze–thaw, and thaw) on soil bacterial community diversity and composition and greenhouse gas emissions during the spring freeze–thaw in the XiLin River riparian wetlands in China by amplicon sequencing and static dark box methods. The results showed that the freeze–thaw periods predominantly impact on the diversity and composition of the bacterial communities. The phyla composition of the soil bacteria communities of the three periods is similar in level, with Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria dominating the microbial communities. The alpha‐diversity of bacterial communities in different periods varies that the freezing period is higher than that of the freeze–thaw period (p <.05). Soil total carbon, soil water content, and microbial biomass carbon were the primary factors regulating the abundance and compositions of the bacterial communities during spring thawing periods. Based on functional predictions, the relative abundance of nitrification and denitrification genes was higher in the freezing period than in the thawing period, while the abundance was lowest in the freeze–thawing period. The correlation results found that N2O emissions were significantly correlated with amoA and amoB in nitrification genes, indicating that nitrification may be the main process of N2O production during spring thaw. This study reveals potential microbial mechanisms of N2O emission during spring thaw and provides data support and theoretical basis for further insight into the mechanism of N2O emission during spring thaw. This study highlights the difference in soil bacterial communities and N cycle functional genes in different spring thawing periods, and the microbial mechanism of N2O during the spring thaw, which is helpful to better understand the microbial process of N2O emission under climate change. [ABSTRACT FROM AUTHOR]

Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened. [ABSTRACT FROM AUTHOR]

Glandora prostrata (Loisel.) D.C.Thomas (Thomas et al., 2008), besides being a common plant of western and south-western Europe and north-western Africa, is a species with a wealth of reported uses in traditional and folk medicine. The chloroplast genome of Glandora prostrata subsp. lusitanica (Samp.) D.C.Thomas (Thomas et al., 2008) isolate BPTPS049 described in this study is the first publicly available complete plastome belonging to the Glandora genus. The chloroplast genome (GenBank accession number: ON641304) is 150,041 bp in length with 37.5% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,833 bp each), separated by a large (81,222 bp) and small (17,153 bp) single-copy regions. It has 131 annotated genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic analysis performed confirms that G. prostrata subsp. lusitanica is placed under the Boraginaceae family, which belongs to the Boraginales order. This study will contribute to conservation, phylogenetic, and evolutionary studies that comprise this traditional species relevant to the landscape of aromatic, medicinal, and condiment plants from Portugal. [ABSTRACT FROM AUTHOR]

TO explore the changes of rhizosphere soil bacterial community of Rosa rugosa "Fenghua", Rosa rugosa cv. Plena and Rosa rugosa "Zizhi" in different seasons, the Illumina Miseq sequencing and the correlation network analysis of dominant flora was used. The results showed that the bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria, with Sphingomonas, GP6, GP4, Novosphingobium, Wps-1_genera_incertae_sedis, and Massilia as the dominant genera. The correlation network analysis showed that, as the dominant group with the highest relative abundance, Sphingomonas had a significant positive correlation with Gemmatimonas, Aridibacter, GP3, GP4, and Flavisolibacter, and a significant negative correlation with Solirubrobacter, indicating that it could work synergistically with a variety of microorganisms to contribute to soil metabolism and the growth and development of roses. The results revealed the diversity of microbial structures in the rhizosphere soil of Rosa rugosa "Fenghua", Rosa rugosa cv. Plena and Rosa rugosa "Zizhi", and this will provide a theoretical basis for exploring the change rules of microbial communities, screening and utilizing beneficial microorganisms, and maintaining the growth and development of roses. Key points: • Variations from season to season significantly affected the bacterial community structure. • There was less variability in the bacterial community structure between rose varieties. • Sphingomonas was the dominant bacterium in all seasons. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Ecology & Rural Environment is the property of Journal of Ecology & Rural Environment Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The rhizosphere of grown tea (Camellia sinensis (L.) O. Kuntze) becomes acidic, and aluminium (Al) toxicity has been identified as a key constraint on plant development in acidic soils. The current study investigated the composition and functions of rhizosphere bacteria as well as soil enzyme activity under different Al stress conditions. The effect of soil pH, soil enzyme activities, the diversity and structure of the rhizosphere bacterial population under various Al concentrations were studied by the pot experiment. All analyses demonstrated that substantial alterations in the activity of soil enzymes and the composition of the bacterial communities in the rhizosphere could only be seen under conditions of extreme Al stress. Soil enzymes were more concentrated in Al concentrations of 100, 150 and 250 µM, respectively. More than 82,000 valid reads were obtained for each replicate, and the abundance of certain genera in the aluminium treated groups were greater than the control group. Lower Al stress attracted Al-tolerant bacteria such as Burkholderia to increase Al stress resistance. These findings revealed that soil enzyme activities and the structure of the rhizosphere bacterial population in tea orchard soil provided tolerance or resistance capability to tea plants for their development under Al stress. [ABSTRACT FROM AUTHOR]

Despite having many historically reported ethnomedicinal uses, Centaurium erythraea Rafn (Rafn and Buchs, 1800; common centaury) also produces cytotoxic secondary metabolites, and its presence should be carefully monitored. In this study, the complete chloroplast of Centaurium erythraea subsp. majus (Hoffmanns. & Link) M.Laínz (Laínz, 1971) isolate BPTPS121 is described, being the first available plastome belonging to the Centaurium genus. The chloroplast genome (GenBank accession number: ) is 153,107 bp in length with 37.9% GC content, displaying a quadripartite structure that contains a pair of inverted repeat regions (25,166 bp each), separated by a large single-copy (84,388 bp) and small single-copy (18,387 bp) regions. A total of 129 genes were predicted, including 37 tRNA genes, eight rRNA genes, and 84 protein-coding genes. The phylogenetic analysis showed that isolate BPTPS121 is placed under the Gentianaceae family, belonging to the Gentianales order. The maximum-likelihood tree supports the already described lineage divergence in the Gentianaceae family, with C. erythraea subsp. majus belonging to the Chironieae tribe positioned below the Exaceae tribe and above the Potalieae and the entire Gentianeae tribes. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food, feed, and supplements safety purposes. [ABSTRACT FROM AUTHOR]

Abstract Background The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources. Results The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks. Conclusions The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%).

The predominantly Western Mediterranean weed Nonea vesicaria (L.) Rchb. can be found in agricultural or other man-made environments. Despite containing some beneficial compounds, extracts from this plant have also been described as detrimental and should be carefully monitored. In this study, the complete chloroplast of N. vesicaria isolate BPTPS250 is described, being the first available plastome from an isolate belonging to the Nonea genus. The chloroplast genome is 151,099 bp in length with a 37.3% GC content. It displays a quadripartite structure that contains a pair of inverted repeat regions (27,012 bp) that separate a large single-copy region (80,041 bp) and a small single-copy region (17,034 bp). A total of 134 genes were predicted, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis confirmed the placement of N. vesicaria under the Boraginaceae family, belonging to the Boraginales order, with a close relationship with Borago officinalis L. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food and feed safety and quality.

Besides being a common weed, the presence of Echium plantagineum L. in food and feed commodities can represent a safety hazard due to their content in pyrrolizidine alkaloids. In this study, the complete chloroplast of E. plantagineum isolate BPTPS251 is described, being the first available plastome from an isolate belonging to the Echium genus. The chloroplast genome is 149,776 bp in length with 37.5% GC content, displaying a quadripartite structure that contains a pair of inverted repeats regions (25,754 bp each), separated by a large single-copy (80,978 bp) and a small single-copy (17,290 bp) regions. A total of 131 genes were predicted, including 37 tRNA genes, 8 rRNA genes, and 86 protein-coding genes. The phylogenetic analysis confirmed the placement of E. plantagineum under the Boraginaceae family, belonging to the Boraginales order. This study will contribute to conservation, phylogenetic, and evolutionary studies, as well as DNA barcoding applications for food and feed safety purposes.

Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors. The assessment was conducted using Illumina MiSeq sequencing in various altitude gradients and on slopes with different aspects (shady slopes and sunny slopes) in the subalpine meadow of Dongling Mountain, Beijing. Topographical factors had a significant effect on soil physicochemical properties: the primary factors determining the structure of microbial communities are total potassium (TK), ammonium nitrogen (NH4+-N), and soil organic carbon (SOC). There was no significant change in the diversity of the bacterial community, whereas the diversity of the fungal community displayed a single-peaked trend. The effect of slope orientation on microbial communities was not as significant as the effect of elevation on them. The number of bacterial communities with significant differences showed a unimodal trend, while the number of fungal communities showed a decreasing trend. The co-occurrence network of fungal communities exhibits greater intricacy than that of bacterial communities, and bacterial communities are more complex in soils with sunny slopes compared to soils with shady slopes, and the opposite is true for fungal communities. The identification of the main factors that control soil microbial diversity and composition in this study, provided the groundwork for investigating the soil microbial response and adaptation to environmental changes in subalpine meadows.

Shaoxing rice wine is a notable exemplar of Chinese rice wine. Its superior quality is strongly correlated with the indigenous natural environment. The results indicated that Firmicutes (75%), Actinobacteria (15%), Proteobacteria (5%), and Bacteroidetes (3%) comprised the prevailing bacterial groups. Among the main bacterial genera, Lactobacillus was the most abundant, accounting for 49.4%, followed by Lactococcus (11.9%), Saccharopolyspora (13.1%), Leuconostoc (4.1%), and Thermoactinomyces (1.1%). The dominant fungal phyla were Ascomycota and Zygomycota. Among the dominant genera, Saccharomyces (59.3%) prevailed as the most abundant, followed by Saccharomycopsis (10.7%), Aspergillus (7.1%), Thermomyces (6.2%), Rhizopus (4.9%), Rhizomucor (2.2%), and Mucor (1.3%). The findings demonstrate that the structure of the bacterial and fungal communities remains stable in the environment, with their diversity strongly influenced by climatic conditions. The continuous fluctuations in environmental factors, such as temperature, air pressure, humidity, rainfall, and light, significantly impact the composition and diversity of microbial populations, particularly the dominant bacterial community.

Sophora alopecuroides L. has great medicinal and ecological value in northwestern China. The host and its microbiota are mutually symbiotic, collectively forming a holobiont, conferring beneficial effects to the plant. However, the analysis of diversity, mycobiota composition, and the ecological function of endophytic fungi in the holobiont of S. alopecuroides is relatively lacking. In this article, the fungal community profiling of roots, stems, leaves, and seeds of S. alopecuroides (at the fruit maturity stage) from Huamachi and Baofeng in Ningxia, China were investigated based on the ITS1 region, using high-throughput sequencing technology. As a result, a total of 751 operational taxonomic units (OTUs) were obtained and further classified into 9 phyla, 27 classes, 66 orders, 141 families, 245 genera, and 340 species. The roots had the highest fungal richness and diversity, while the stems had the highest evenness and pedigree diversity. There also was a significant difference in the richness of the endophytic fungal community between root and seed (p < 0.05). The organ was the main factor affecting the community structure of endophytic fungi in S. alopecuroides. The genera of unclassified Ascomycota, Tricholoma, Apiotrichum, Alternaria, and Aspergillus made up the vast majority of relative abundance, which were common in all four organs as well. The dominant and endemic genera and biomarkers of endophytic fungi in four organs of S. alopecuroides were different and exhibited organ specificity or tissue preference. The endophytic fungi of S. alopecuroides were mainly divided into 15 ecological function groups, among which saprotroph was absolutely dominant, followed by mixotrophic and pathotroph, and the symbiotroph was the least. With this study, we revealed the diversity and community structure and predicted the ecological function of the endophytic fungi of S. alopecuroides, which provided a theoretical reference for the further development and utilization of the endophytic fungi resources of S. alopecuroides. [ABSTRACT FROM AUTHOR]

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Soil microorganisms play crucial roles in nutrient cycling and determining soil quality and fertility; thus, they are important for agricultural production. However, the impacts of long-term fertilization on soil microbial community remain ambiguous due to inconsistent results from different studies. The objective of this study was to characterize changes in bacterial and fungal diversity and community structures after 12 years of different fertilization in aeolian sandy soil by analyzing 16S rRNA and ITS rRNA gene sequences and the soil properties to discover the driving factors. Eight different fertilizer treatments have been set up since 2009: no fertilizer (CK), chemical N fertilizer (N), chemical N and P fertilizer (NP), chemical N, P and K fertilizer (NPK), pig manure only (M), pig manure plus chemical N fertilizer (MN), pig manure plus chemical N and P fertilizer (MNP), pig manure plus chemical N, P, and K fertilizer (MNPK). The results indicated that the long-term application of chemical fertilizer reduced soil pH, whereas the addition of pig manure alleviated a decrease in soil pH value. Chemical fertilizer plus pig manure significantly improved soil available nutrients and soil organic carbon. Long-term MNPK fertilization resulted in changes in bacterial diversity due to effects on specific bacterial species; by contrast, all fertilization treatments resulted in changes in fungal diversity due to changes in soil properties. Principal component analysis indicated that fertilization had a significant effect on soil microbial community structure, and the effect of chemical fertilizer combined with pig manure was greater than that of chemical fertilizer alone. Soil available phosphorus, total phosphorus, and pH were the most important factors that influenced bacterial taxa, whereas soil pH, total phosphorus, organic carbon, ammonium nitrogen and nitrate nitrogen were the most important factors influencing fungal taxa after 12 years of fertilization in aeolian sandy soil. [ABSTRACT FROM AUTHOR]

The agricultural irrigation and fertigation systems have a non-negligible impact on the soil microenvironment in arid and semi-arid areas. Therefore, studying the processes and changes of soil microenvironment under different plastic mulch drip irrigation systems can reveal the "soil-microbe" mechanism and provide a theoretical support for the optimal irrigation and nutrition management of maize in the semi-arid area of Northeast China. Three treatments were used for this study in the semi-arid area of northeast China, namely; mulched fertigation system (MF), drip irrigation system (DI), and farmers' practices system (FP). Weused high-throughput sequencing to study the soil bacterial community structure targeting the 16S rRNA gene. The agricultural irrigation and fertigation systems significantly affected soil properties. MF significantly increased bacterial abundance and bacterial diversity and richness. Moreover, MF and DI markedly increased some relative abundance of beneficial bacterial. The bacterial network in MF was more conducive to the health and stability of the agroecosystem and the relationships among species in MF bacterial network were more complex. The agricultural irrigation and fertigation systems had indirect effects on community composition and bacterial diversity through soil organic carbon (SOC), ammonium nitrogen (NHC4 -N), nitrate nitrogen (NO3 -N), pH, moisture, NHC4 -N and NO3 -N had indirect effects on yield through bacterial community composition, bacterial diversity and bacterial abundance. These findings suggested that MF was the most effective treatment to improve soil bacterial abundance and diversity, and stabilize the functional quality of soil biological processes. [ABSTRACT FROM AUTHOR]

The increased population density of rodent species during ongoing grassland degradation further deteriorates its conditions. Understanding the effects of grassland degradation on rodent feeding habits is of great value for optimizing grassland management strategies. In this study, lightly degraded (LD), moderately degraded (MD), severely degraded (SD), and reseeded grassland (RG) were selected and their plant resources and soil physical properties were investigated. In addition, the study used ITS2 barcode combined with the Illumina MiSeq sequencing method to analyze the food composition and proportion of plateau zokors in different grassland conditions. The results showed that, with grassland degradation, plant biomass decreased, but the relative proportion of forbs increased (LD: 32.05 ± 3.89%; MD: 28.97 ± 2.78%; SD: 49.16 ± 4.67% and RG: 10.93 ± 1.53%). Forbs were the main food of the plateau zokor, accounting for more than 90% of their diet, and the animal had a clear preference for Potentilla species; the soil compaction of feeding habits showed a decreasing trend in the 10–25 cm soil layer, suggesting a decreased foraging cost. Nutritional analysis showed that the stomach content of crude protein in zokors feeding on MD grassland was significantly higher than that of animals feeding on the other grassland types. Structural equation modeling showed that soil physical properties and the relative biomass of forbs had significant (P < 0.05) and extremely significant (P < 0.001) impacts on the population density of plateau zokors, with direct impact contribution rates of 0.20 and 0.63. As the severity of grassland degradation increased, although the aboveground and underground biomass of the plants decreased, the proportion of food preferred by the plateau zokor increased, and the corresponding changes in the feeding environment resulted in decreased foraging energy expenditure, thereby increasing the suitability of the degraded grassland for the plateau zokor. Compared with degraded grassland, the food diversity and evenness of zokors increased, the food niche width enlarged, and the proportion of weeds decreased in RG, which increased the difficulty of obtaining food. Reseeding in grassland management is therefore an effective way to control plateau zokors.

We studied the succession of bacterial communities during the biodegradation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD). The communities originated from a mesocosm with soil from Bien Hoa airbase in Vietnam heavily contaminated with herbicides and dioxins. They were grown in defined media with different carbon and Gibbs energy sources and 2,3,7,8-TCDD. Cultures with dimethyl sulfoxide (DMSO) as the sole carbon and energy source degraded about 95% of 2,3,7,8-TCDD within 60 days of cultivation. Those with an additional 1 mM of vanillin did that in roughly 90 days. Further 16S rRNA gene amplicon sequencing showed that the increase in relative abundance of members belonging to the genera Bordetella, Sphingomonas, Proteiniphilum, and Rhizobium correlated to increased biodegradation of 2,3,7,8-TCDD in these cultures. A higher concentration of vanillin slowed down the biodegradation rate. Addition of alternative carbon and Gibbs energy sources, such as amino acids, sodium lactate and sodium acetate, even stopped the degradation of 2,3,7,8-TCDD completely. Bacteria from the genera Bordetella, Achromobacter, Sphingomonas and Pseudomonas dominated most of the cultures, but the microbial profiles also significantly differed between cultures as judged by non-metric multidimensional scaling (NMDS) analyses. Our study indicates that 2,3,7,8-TCDD degradation may be stimulated by bacterial communities preadapted to a certain degree of starvation with respect to the carbon and energy source. It also reveals the succession and abundance of defined bacterial genera in the degradation process. [ABSTRACT FROM AUTHOR]

Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson's correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to Planococcaceae , Bacillaceae , Woeseiaceae and Rhodobacteraceae. Furthermore, Planococcaceae , Bacillaceae , Woeseiaceae and Rhodobacteraceae were closely related to grape nutrient absorption and fruit quality. Bacillaceae and Woeseiaceae were positively correlated with total soluble sugar, while Planococcaceae and Rhodobacteraceae were positively correlated with titratable acid. Hence, Bacillaceae and Woeseiaceae were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer. [ABSTRACT FROM AUTHOR]

High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS. With this in mind, a study was completed, comparing the most established HTS platform (MiSeq benchtop sequencer—Illumina), with the MinION sequencer (Oxford Nanopore Technologies) for the detection of plant viruses and viroids. Method comparisons were performed on five selected samples, containing two viroids, which were sequenced using nanopore technology for the first time and 11 plant viruses with different genome organizations. For all samples, sequencing libraries for the MiSeq were prepared from ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) and for MinION sequencing, direct RNA sequencing of totRNA was used. Moreover, for one of the samples, which contained five different plant viruses and a viroid, three additional variations of sample preparation for MinION sequencing were also used: direct RNA sequencing of rRNA-depleted totRNA, cDNA-PCR sequencing of totRNA, and cDNA-PCR sequencing of rRNA-depleted totRNA. Whilst direct RNA sequencing of total RNA was the quickest of the tested approaches, it was also the least sensitive: using this approach, we failed to detect only one virus that was present in a sample at an extremely low titer. All other MinION sequencing approaches showed improved performance with outcomes similar to Illumina sequencing, with cDNA-PCR sequencing of rRNA-depleted totRNA showing the best performance amongst tested nanopore MinION sequencing approaches. Moreover, when enough sequencing data were generated, high-quality consensus viral genome sequences could be reconstructed from MinION sequencing data, with high identity to the ones generated from Illumina data. The results of this study implicate that, when an appropriate sample and library preparation are selected, nanopore MinION sequencing could be used for the detection of plant viruses and viroids with similar performance as Illumina sequencing. Taken as a balance of practicality and performance, this suggests that MinION sequencing may be an ideal tool for fast and affordable virus diagnostics. [ABSTRACT FROM AUTHOR]