[Effects of Biogas Slurry Application on Soil Microbial Communities Structure and Function During Wheat-rice Stubble Period]

To reveal the effects of biogas slurry application on soil microbial community structure and function, a soil column experiment was constructed with three treatments[(no N addition, CM; conventional fertilization, SN; biogas slurry addition, SZ)]. The differences in composition, diversity, and structure of bacterial and fungal communities on day 1 and day 21 after soil flooding were evaluated, and their functions were predicted using Illumina high-throughput sequencing technology. The results of the analysis of α diversity showed that the fungal α-diversity indexes of CM, SN, and SZ treatments on day 1 were significantly higher than those on day 21, and there was no significant difference among the three treatments. However, the bacterial Simpson index differed among the three treatments on day 21, with SZ-21 showing a higher Simpson index but lower Chao1 index compared with those of SZ-21. The analysis of bacterial community structure showed that Firmicutes, Chloroflexi, and Actinobacteria in the SN-1 treatment were different from those in the other treatments on day 1, whereas the relative abundance of bacterial phyla in the SZ and SN treatments were similar on day 21. The analysis of fungal community structure showed that the relative abundance of Ascomycota and Zygomycota in the SZ-1 treatment were higher than those in the SN-1 and CM-1 treatments on day 1. The relative abundance of Ascomycota in the SN-21 and SZ-21 treatments were lower, whereas that of Zygomycota were higher compared with that in CM-21. The analysis of NMDS showed that the composition of bacterial and fungal communities in the SN and SZ treatments showed a gradually similar trend. The PICRUSt analysis showed that the function of the soil bacterial community was similar in the CM, SN, and SZ treatments. The FUNGuild function prediction reflected that the main differences in trophic type between the SN-21 and SZ-21 treatments occurred in saprotroph and pathotroph forms. Therefore, biogas slurry addition in the wheat-rice stubble stage could contribute to balancing soil nutrients and maintaining soil ecological function to a certain extent, but there may still be a risk of fungal disease.

Ecological risk assessment and identification of the distinct microbial groups in heavy metal-polluted river sediments

To assess the health of river ecosystems, it is essential to quantify the ecological risk of heavy metals in river sediments and the structure of microbial communities. As important tributaries of the Tuo River in the upper reaches of the Yangtze River, the Mianyuan River and the Shiting River, are closely related to the economic development and human daily life in the region. This study assessed the ecological risks of heavy-metal-polluted river sediments, the heavy-metal-driven bacterial communities were revealed, and the relationships between the ecological risks and the identical bacterial communities were discussed. The Cd content was significantly greater than the environmental background value, leading to a serious pollution and very high ecological risk at the confluence of the two rivers and the upper reaches of the Mianyuan River. Microbial community analysis showed that Rhodobacter, Nocardioides, Sphingomonas, and Pseudarthrobacter were the dominant bacterial genera in the sediments of the Shiting River. However, the dominant bacterial genera in the Mianyuan River were Kouleothrix, Dechloromonas, Gaiella, Pedomicrobium, and Hyphomicrobium. Mantel test results showed (r = 0.5977, P = 0.005) that the Cd, As, Zn, Pb, Cr, and Cu were important factors that influenced differences in the distribution of sediment bacterial communities Mianyuan and Shiting rivers. A correlation heatmap showed that heavy metals were negatively correlated for most bacterial communities, but some bacterial communities were tolerant and showed a positive correlation. Overall, the microbial structure of the river sediments showed a diverse spatial distribution due to the influence of heavy metals. The results will improve the understanding of rivers contaminated by heavy metals and provide theoretical support for conservation and in situ ecological restoration of river ecosystems.

Distribution of sediment microbial communities and their relationship with surrounding environmental factors in a typical rural river, Southwest China

With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Firmicutes, accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae, Haliangium, and Pseudolabrys, possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola, Nocardioides, Gaiella, Sphingomonas, norank_f_67-14, Subgroup_10, Agromyces, and Lysobacter, with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1, norank_f__Bacteroidetes_vadinHA17, Candidatus_Competibacter, and Methylocystis. Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.

Construction and characterization of microsatellite markers for the Neptune whelk, Neptunea cumingii

BACKGROUND

The Neptune whelk, Neptunea cumingii, is an economic gastropod endemic to the East Asia Warm Temperate Biotic Subregion. The study of the development in microsatellite markers maybe beneficial for assessing the genetic diversity and conservation of resources on this dwindling species.

METHODS AND RESULTS

The microsatellite markers were constructed and characterized through Illumina high-throughput sequencing and capillary electrophoresis techniques. Eleven polymorphic microsatellite loci were screened and validated. The observed heterozygosity and expected heterozygosity of each locus showed a range from 0.0600 to 0.6508 and from 0.7380 to 0.9375, respectively. The average Shannon's information index and polymorphism information content were 2.0828 and 0.8325, respectively. Deviation from all loci was generated from Hardy-Weinberg equilibrium.

CONCLUSIONS

The 11 microsatellite markers developed in this study show polymorphic status. These markers are expected to be highly informative for further analysis of genetic diversity in N. cumingii.

Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas

Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.

[Characteristic Analysis of nirS Denitrifying Bacterial Community in Lijiahe Reservoir During Stratification]

To explore the composition of the nirS denitrifying bacterial community during stratification in spring(March to May) in a drinking water reservoir and its relationship with water quality, the water quality and relative abundance and structure of the denitrifying bacterial community were analyzed using in-situ monitoring coupled with Illumina high-throughput sequencing technology in the Lijiahe Reservoir. The results showed that:① through high-throughput sequencing, 4 phyla and 13 genera were identified. The dominant bacterial phylum was Proteobacteria, and its relative abundance was between 52.5% and 70.6%. The overall trend of the relative abundance of Proteobacteria decreased on the time scale (P<0.05), and its relative abundance in the surface and middle layers was higher than that of the bottom layer on the spatial scale (P<0.05). There was no difference in the proportion of Proteobacteria between the surface and middle layers (P>0.05), and the abundance of its bottom layer was relatively stable; eight genera of bacteria with denitrification function were identified, among which the dominant bacterial genera (relative abundance>1%) were Dechloromonas and Pseudomonas. The relative abundance of Dechloromonas showed a trend of first decreasing and then increasing on the time scale, whereas the relative abundance of Pseudomonas showed a trend of increasing first and then decreasing on the time scale. There were no differences on the spatial scale between these two genera (P>0.05); the changes in bacterial diversity and abundance were basically similar, with a trend of first increasing and then decreasing on the time scale. The highest diversity and abundance of the bacterial community gradually increased with increasing depth on the spatial scale. ② ρ(TN) of the reservoir during stratification was 2.35-2.91 mg·L^-1, and the nitrogen pollution was more serious. In March and April, ρ(TN) on the vertical scale was basically similar and showed a decreasing trend. In May, the content of total nitrogen was higher than that in March and April, and the highest value of total nitrogen content occurred in the surface layer. ③ Redundancy analysis showed that water temperature, dissolved oxygen, nitrate, and ammonia nitrogen were the main driving factors, and ammonia nitrogen showed a significantly negative correlation with Dechlormonas. In summary, the study of nirS-type denitrification communities and related influencing factors will contribute to analyzing the characteristics of denitrifying bacterial community changes in a micro-polluted drinking water reservoir and provide a theoretical research basis for the biological remediation of nitrogen pollution in such reservoirs in the future.

Succession of Fungal Communities at Different Developmental Stages of Cabernet Sauvignon Grapes From an Organic Vineyard in Xinjiang

Fungi present on grape surface considerably impact grape growth and quality. However, information of the fungal community structures and dynamics on the worldwide cash crop, the Cabernet Sauvignon grape, from the budding to ripening stages remains limited. Here, we investigated the succession of fungal communities on Cabernet Sauvignon grapes from an organic vineyard in Xinjiang, China at different developmental stages via high-throughput sequencing combined with multivariate data analysis. In total, 439 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal communities differed over the budding to the berry stages. Moreover, Aspergillus, Malassezia, Metschnikowia, and Udeniomyces were predominant during the unripe stage, whereas Erysiphe, Cryptococcus, Vishniacozyma, and Cladosporium were dominant in the ripe stages. Notably, Vishniacozyma was the most abundant genus, conserved in all development stages. Moreover, network analysis resulted in 171 edges—96 negative and 75 positive. Moreover, fungal genera such as Vishniacozyma, Sporobolomyces, Aspergillus, Alternaria, Erysiphe, Toxicodendron, and Metschnikowia were present in the hubs serving as the main connecting nodes. Extensive mutualistic interactions potentially occur among the fungi on the grape surface. In conclusion, the current study expounded the characteristics of the Cabernet Sauvignon grape fungal community during the plant growth process, and the results provided essential insights into the potential impacts of fungal communities on grape growth and health.

Effects of chloropicrin fumigation combined with biochar on soil bacterial and fungal communities and Fusarium oxysporum

Chloropicrin (CP) can cause long-term damage to beneficial microbes which reduces soil health. Biochar (BC) can mitigate against the effects of CP by reducing the time for beneficial microbes to recover after CP fumigation. In this study, we used Real-Time Quantitative PCR to determine the effects of different rates of BC added to CP-fumigated soil on the speed of recovery of bacteria and fungi population and on changes to gene copy number of the target pathogen Fusarium oxysporum. And then we compared the structure and composition of the beneficial microbial community in the different treatments soil by using High throughput Illumina sequencing. As the results shown, adding 1 or 3% BC after CP fumigation accelerated the recovery of bacterial and fungal populations without increasing F. oxysporum abundance. BC also promoted the recovery of beneficial bacteria Rokubacteria and Latescibacteria damaged by CP. And these two bacteria may be related to the immunity of soil to F. oxysporum. In CP-fumigated soil, BC improved the disease resistance of the soil by increasing beneficial microbes, such as Steroidobacter, Sphingomonas, Purpureocillium and Mortierella. This combination of CP and BC is a new concept that could encourages the development of a healthy and sustainable soil ecosystems while controlling plant pathogens.

Response of Root-Associated Bacterial Communities to Different Degrees of Soft Rot Damage in Amorphophallus konjac Under a Robinia pseudoacacia Plantation

Bacterial soft rot is a destructive disease that restricts the development of the konjac (Amorphophallus konjac K. Koch ex N.E.Br) industry. The objective of this study was to investigate how soft rot disease affects bacterial communities associated with the roots of konjac plants growing under a pure Robinia pseudoacacia plantation. Three sampling sites affected by different degrees of soft rot damage were selected based on the disease incidence [0%, non-diseased (ND); 4.2%, moderately diseased (MD); and 18.6%, highly diseased (HD)]. The variation in soil and root bacterial diversity and community composition among the sampling sites was determined by Illumina HiSeq sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. The results showed that the contents of soil organic matter and available nutrients (N, P, and K) increased with increasing damage degree, whereas higher damage degree resulted in lower soil pH and enzymatic activity (sucrase, urease, catalase, and polyphenol oxidase). The composition of root-associated bacterial communities differed among the three sampling sites. Proteobacteria was the most dominant bacterial phylum in all soil and root samples. Pseudomonas, Bacillus, Rhizobium, and Streptomyces were the most abundant in all samples from the ND sites, whereas Pectobacterium carotovorum and Serratia were predominant in the samples from the MD and HD sites. The abundance and alpha diversity of root-associated bacteria were significantly higher (p < 0.05) in the ND sites than in the diseased sites. The results suggested pronounced differences in the abundance, alpha diversity, and community composition of bacteria associated with the roots of konjac plants affected by different degrees of soft rot damage. Such differences in bacterial community structure were related to dynamic changes in soil variables, especially soil available potassium content, sucrase activity, and urease activity. Analysis of the dominant root-associated bacterial taxa offers an approach to predict the damage degree due to soft rot in konjac and provides evidence for the prevention of this soil-borne disease via microecological regulation.

Fungal community diversity and fermentation characteristics in regional varieties of traditional fermentation starters for Hong Qu glutinous rice wine

Hong Qu glutinous rice wine (HQ wine) is a traditional alcoholic beverage produced in China by fermenting cooked rice using a fermentation starter prepared with the fungus Monascus purpureus. This starter (Hong Qu, HQ) is made empirically by open spontaneous fermentation that is hard to control and standardize, resulting in inconsistent wine quality. This study investigates representative HQ samples from a large geographic region. It explores fungal microbiome compositions, identifies characteristic differences important for the production of various HQ wine styles, and reveals the key fungi responsible for HQ wine fermentation characteristics. The source of the HQ inoculum was found to be the main factor influencing fungal community composition and diversity, followed by processing technology and geographical distribution. Linear discriminant analysis effect size (LEfSe) uncovered 14 genera as potential biomarkers to distinguish regional varieties of HQ. Significant differences were also found in fermentation characteristics such as liquefying power (LP), saccharifying power (SP), fermenting power (FP), total acid content (TA) and liquor-producing power (LPP). The key fungi responsible for LP (5 genera), SP (3 genera), FP (1 genera), LPP (4 genera), and TA (4 genera) were determined using redundancy correlation analysis. Finally, Spearman's correlation analysis indicated that LPP shows a strong positive correlation with FP and LP, while TA displays a strong negative correlation with FP. The results of this study may be utilized to prepare consistently high quality, next-generation HQ by better controlling fungal community structures, and to design fermentation processes for HQ wines with desirable oenological characteristics.

Contribution of influent rivers affected by different types of pollution to the changes of benthic microbial community structure in a large lake

As a microbial group in watershed ecosystems, the bacterial community is a sensitive indicator of external environmental fluctuations. However, the effects of different sources of exogenous pollution on the diversity and structure of bacterial communities in inflow rivers and lakes have not been studied in depth. In this study, we used 16S rRNA gene sequencing technology to study the diversity and composition of bacterial communities in rivers affected by different types of pollution. The results showed that the composition of the bacterial communities in rivers with different exogenous pollution sources was different. For example, the genus Arenimonas, which belongs to the Gamma-proteobacteria, is extensively enriched in IDPR (industrially and domestically polluted rivers) and ADPR (agriculturally and domestically polluted rivers) (KW, p < 0.05), while the genus Micromonospora is a more unique genus found in APR (agriculturally polluted rivers). When exploring the topology and classification characteristics of river microbial symbiosis models, it was found that the bacterial community symbiosis network is divided into six modules under different exogenous pollution regimes, and the nodes in the different modules perform different functions, such as the IDPR-dominated module I. In the network, the relatively abundant the genus Flavobacterium and the genus Nitrospira are the key factors driving the nitrogen cycle in the watershed where the samples were collected. In addition, our research indicates that communities in lake environments may be more susceptible to disturbances of various physiological or functional redundancies, thus retaining their original community structure. Overall, this study emphasizes that adaptive changes in the bacterial community structure of the sediments in the catchment and the occurrence of interactions are responses to different exogenous pollution sources.

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America

Spatial patterns of bacterial community composition often follow a distance-decay relationship in which community dissimilarity increases with geographic distance. Such a relationship has been commonly observed in natural environments, but less so in engineered environments. In this study, bacterial abundance and community composition in filter media samples (n = 57) from full-scale rapid biofilters at 14 water treatment facilities across North America were determined using quantitative polymerase chain reaction and Illumina HiSeq high-throughput sequencing targeting the 16S rRNA gene, respectively. Bacteria were abundant on the filter media (108.8±0.3 to 1010.7±0.2 16S rRNA gene copies/cm3 bed volume) and the bacterial communities were highly diverse (Shannon index: 5.3 ± 0.1 to 8.4 ± 0.0). Significant inter-filter variations in bacterial community composition were observed, with weighted UniFrac dissimilarity values following a weak but highly significant distance-decay relationship (z = 0.0057 ± 0.0006; P = 1.8 × 10-22). Approximately 50% of the variance in bacterial community composition was explained by the water quality parameters measured at the time of media sample collection (i.e. pH, temperature and dissolved organic carbon concentration). Overall, this study suggested that the microbiomes of biofilters are primarily shaped by geographic location and local water quality conditions but the influence of these factors on the microbiomes is tempered by filter design and operating conditions.

[Community Structure Characteristics of nirS Denitrifying Bacteria of Spring Typical Parkland Waterbodies in Shijiazhuang City]

Four typical park water bodies located in the main urban area of Shijiazhuang city were selected to study the relationships between water quality and the community structure and diversity of nirS denitrifying bacteria. The results showed that the nitrogen concentration ranged from 4.43 to 13.83 mg·L^-1 in four park water bodies, which exhibited notable nitrogen pollution characteristics. Based on the characteristic index analysis of three-dimensional fluorescence spectra, the four park water bodies all exhibited strong autochthonous components and low humus characteristics. The results of Illumina high-throughput sequencing indicated that most of the nirS denitrifying bacteria showed significant differences in dominant genus. The unclassified_Bacteria (53.52%), Pseudomonas (60.48%), and Rhodobacter (46.94%) were the dominant bacteria in Yuxi park, Shuishang park, and Chang'an park, respectively. In comparison, unclassified_Bacteria (36.19%) and unclassified_Proteobacteria (23.44%) were the dominant bacteria in Shiji park. Redundancy analysis showed that denitrification bacteria in Yuxi park were mainly affected by nitrate, total nitrogen, and dissolved oxygen; denitrification bacteria in Shuishang park were greatly affected by total phosphorus; denitrification bacteria in Chang 'an park were mainly affected by ammonia and nitrous nitrogen; and denitrification in Shiji park were mainly affected by total phosphorus, nitrite, and ammonia. Overall, the water quality and the community structure of nirS denitrification bacteria exhibited significant differences in park water bodies. Further research could contribute to the understanding of water quality characteristics and the denitrifying community structure of urban water systems, and develop efficient denitrifying bacterial agents.

Effect of chemical oxygen demand load on the nitrification and microbial communities in activated sludge from an aerobic nitrifying reactor

In this study, we explored the effect of chemical oxygen demand (COD) load on the nitrification and microbial communities in activated sludge isolated from an aerobic nitrifying tank. The activated sludge was cultured in three different COD groups: L-COD, 200 mg/L; M-COD, 1200 mg/L; H-COD, 4200 mg/L. The results indicated that the COD exerts a negligible effect on the nitrogen removal ability within the first 24 h. However, the nitrification rate decreased with culture time; the ammonium degradation rates were found to be 80.26%, 57.56%, and 43.43% at 72 h in the three COD groups, respectively. These values correspond to decreases of 19.40%, 41.83%, and 51.48%, respectively, in relation to those observed at 24 h. The activated sludge in the different COD groups exhibited similar community compositions after 24 h, as assessed by Illumina high-throughput sequencing, while a significant difference in the relative abundances of some organisms occurred after 48 and 72 h. Proteobacteria was the main phylum, with a relative abundance of >51.45%. The genera Aridibacter, Paracoccus, Nitrospira, and Nitrosomonas were suppressed by COD load over time. This study may contribute to our knowledge about the nitrification ability and microbial communities in activated sludge at different COD load levels.

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China

Sediment bacterial communities are critical for the circulation of nutrients in lake ecosystems. However, the bacterial community function and co-occurrence models of lakes have not been studied in depth. In this study, we observed significant seasonal changes and non-significant spatial changes in the beta diversity and community structure of sediment bacteria in Lake Chaohu. Through linear discriminant analysis effect size (LEfSe), we observed that certain taxa (from phylum to genus) have consistent enrichment between seasons. The sudden appearance of a Firmicutes population in spring samples from the Zhaohe River, an estuary of Lake Chaohu, and the dominance of Firmicutes populations in other regions suggested that exogenous pollution and environmental induction strongly impacted the assembly of bacterial communities in the sediments. Several taxa that serve as intermediate centers in Co-occurrence network analysis (i.e., Pedosphaeraceae, Phycisphaeraceae, Anaerolineaceae, and Geobacteraceae) may play an important role in sediments. Furthermore, compared with previous studies of plants and animals, the results of our study suggest that various organisms, including microorganisms, are resistant to environmental changes and/or exogenous invasions, allowing them to maintain their community structure.

Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing

Insight to nitrogen transformation and cycling during composting is vital in developing management strategies that improve nitrogen content and quality of the end product. In this study, a positive ventilation device was constructed and used to elucidate nitrogen transformation and microbial community structures during the composting of cow manure and rice straw. Bacterial community successions were analyzed during the composting process by examining the change in their structural dynamics using high-throughput sequencing technique. The results revealed that dominant phyla, included Acidobacter, Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Actinobacteria. Furthermore, a positive strong correlation was observed between the key bacterial communities and nitrogen transformation. Analyses of functional genera, Spearman correlation and Path showed that Thermomonospora_curvata_DSM_43183 followed by Luteimonas and Simiduia, Brevundimonas and Tamlana, Pseudomonas followed by Brevundimonas and Flavobacterium were the key bacterial communities affecting NH₄⁺-N, NO₃^--N, and NO₂^--N transformation, respectively. Thauera followed by Pseudomonas_putida_NBRC_14164 played a dominant role in N₂O transformation.

[Elevational Distribution Characteristics of Soil Bacterial Community and Enzyme Activities in Mount Huangshan]

Mount Huangshan has a well-preserved ecosystem and obvious differences in vertical geography, which provide a natural laboratory for studying the altitudinal distribution patterns of soil microbial communities in a mid-subtropical forest ecosystem. The soil bacterial community structure and diversity of the samples collected every 100 m from 670 to 1870 m on the south slope of Mount Huangshan were examined using Illumina MiSeq high-throughput sequencing technology. The soil physicochemical properties and soil enzyme activities of the samples were also measured to explore the relationship between bacterial communities and soil properties as well as enzyme activities. The results showed that ① The contents of soil total nitrogen, available nitrogen, total potassium, and total organic carbon were significantly different across the altitudes (P<0.01) and generally increased as altitude increased. The soil sucrase activities across altitudes were significantly different (P<0.01), and generally increased as altitude increased. However, there was no significant difference in acid phosphatase and urease activities between different altitudes (P>0.05). ② The 12 elevational gradients were divided into three groups:low altitude (670-875 m), medium altitude (1080-1370 m), and high altitude (1460-1780 m). The OTUs in low altitude sites were greater than in high altitude sites but lower compared to medium altitude sites. However, the differences in OTUs across altitude sites were not significant. ③ The soil bacterial community diversity showed a unimodal pattern in a small range of altitudes from 875-1370 m, although no apparent trend was observed at the altitudes from 670-1780 m. ④ There were 7 dominant phyla and 15 dominant orders with a relative abundance of more than 3% in all soil samples. ⑤ Correlation heat map analysis between the top 15 bacterial phyla and soil physicochemical properties as well as enzyme activities showed that soil pH had the greatest effect on the differences in soil bacterial community structure across the different altitudes. Pearson correlation analysis and Partial Mantel test also showed that bacterial community α-diversity (P<0.01) and β-diversity (Partial Mantel r=0.560, P=0.001) were mainly affected by soil pH. Consequently, soil pH was the key environmental factor determining the soil bacterial community structure and diversity across the different altitudes on Mount Huangshan.

Monitoring microbial communities' dynamics during the start-up of microbial fuel cells by high-throughput screening techniques

Microbial Electrochemical Technologies are based on the use of electrochemically active microorganisms that can carry out extracellular electron transfer to an electrode while they are oxidizing the organic compounds. The dynamics and changes of the bacterial community in the anode biofilm and planktonic broth of an acetate fed batch single chamber air cathode MFC have been studied by combing flow-cytometry and Illumina sequencing techniques. At the beginning of the test, from 0 h to 70 h, microbial planktonic communities changed from four groups to two groups, as revealed by DNA content, and from three groups to one group based on the cell membrane polarization revealed by a DiOC₆(3) probe. Between 4^th day and 13^th day, microbial communities changed from one group to a maximum of three groups, monitoring DNA content, and from one group to two based on the cell membrane polarization. The 16S rDNA gene profiling confirmed the shift in microbial communities, with Acinetobacter (39.34%), Azospirillum (27.66%), Arcobacter (4.17%) and Comamonas (2.62%) being the most abundant genera at the beginning of MFC activation. After 70 h the main genera detected were Azospirillum (46.42%), Acinetobacter (34.66%), Enterococcus (2.32%), Dysgonomonas (2.14%). Data obtained have shown that flow cytometry and illumina sequencing are useful tools to monitor "online" the changes in microbial communities during the MFCs start-up and the increase of Azospirillum and Acinetobacter genera is in good agreement with the MFC voltage generation. Moreover, monitoring planktonic populations, instead of the less accessible anode biofilm, was in good agreement with the evolution of MFC voltage.

High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens

The microbial community structures of drinking water treatment sludge (DWTS) generated for raw water (RW) from different locations and with different source types - including river water, lake water and reservoir water -were investigated using high-throughput sequencing. Because the unit operations in the six DWTPs were similar, community composition in fresh sludge may be determined by microbial community in the corresponding RW. Although Proteobacteria, Cyanobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Planctomycetes were the dominant phyla among the six DWTS samples, no single phylum exhibited similar abundance across all the samples, owing to differences in total phosphorus, chemical oxygen demand, Al, Fe, and chloride in RW. Three genera of potentially toxic cyanobacteria (Planktothrix, Microcystis and Cylindrospermopsis), and four potential pathogens (Escherichia coli, Bacteroides ovatus, Prevotella copri and Rickettsia) were found in sludge samples. Because proliferation of potentially toxic cyanobacteria and Rickettsia in RW was mainly affected by nutrients, while growth of Escherichia coli, Bacteroides ovatus and Prevotella copri in RW may be influenced by Fe, control of nutrients and Fe in RW is essential to decrease toxic cyanobacteria and pathogens in DWTS.

Archaeal community compositions in tilapia pond systems and their influencing factors

Archaea, like the bacterial communities are gradually being realized as key players in the biogeochemical progress of water ecosystems. In this study, tilapia aquaculture ponds were used for an in-depth understanding of archaeal community compositions in water and surface sediment. Some of the main functions, as well as the communities' response patterns, to time variations, pond differences and some physio-chemical parameters were investigated. The results revealed the dominant phylum in both the water and surface sediment, as Euryarchaeota, while, the most abundant classes were: Halobacteria and Methanomicrobia respectively. Significant differences in the archaeal community compositions in the water and surface sediment, were observed in the early stages of cultivation, which became minimal at the later stage of the GIFT tilapia cultivation. Additionally to the differences in the most abundant classes, more OTUs were observed in water samples than in surface sediment samples. The methane generation could be attributed to the large proportion of methanogens found in both pond water and in the surface sediment. Furthermore, the archaeal community compositions in water and the surface sediment were shaped mainly by temporal variations and pond differences respectively. In the pond water, the archaeal community compositions were highly co-related to the concentration changes of ammonia, sulfate and total nitrogen; while in the surface sediment, the correlation to the content changes was significant in total phosphorus. The archaeal community compositions in surface sediment should be considered as an indicator for future environmental capacity studies in aquaculture.

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions

Wastewater treatment plants (WWTPs) in plateau regions have unique microbial community structures. In this study, Illumina high-throughput sequencing technology was applied to investigate microbial communities of plateau WWTPs. The research showed that microbial diversities and richness were negatively associated with the altitude and positively to the water temperature to a certain extent. The dominant phyla of plateau and control WWTPs were similar, which mainly included Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. In plateau WWTPs, the LEfSe analysis found 4 biomarkers which can catabolize aromatic compounds, indicating the microorganisms that can degrade refractory organics might survive better in plateau WWTPs. The analysis of functional genera and enzymes showed that there was no significant difference in abundances of organic degrading bacteria, but the nitrogen removal bacteria were less abundant and phosphorus removal bacteria were more abundant in plateau WWTPs.

Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment

The microbial community diversity in anaerobic-, anoxic- and oxic-biological zones of a conventional Carrousel oxidation ditch system for domestic wastewater treatment was systematically investigated. The monitored results of the activated sludge sampled from six full-scale WWTPs indicated that Proteobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Verrucomicrobia, Acidobacteria and Nitrospirae were dominant phyla, and Nitrospira was the most abundant and ubiquitous genus across the three biological zones. The anaerobic-, anoxic- and oxic-zones shared approximately similar percentages across the 50 most abundant genera, and three genera (i.e. uncultured bacterium PeM15, Methanosaeta and Bellilinea) presented statistically significantly differential abundance in the anoxic-zone. Illumina high-throughput sequences related to ammonium oxidizer organisms and denitrifiers with top50 abundance in all samples were Nitrospira, uncultured Nitrosomonadaceae, Dechloromonas, Thauera, Denitratisoma, Rhodocyclaceae (norank) and Comamonadaceae (norank). Moreover, environmental variables such as water temperature, water volume, influent ammonium nitrogen, influent chemical oxygen demand (COD) and effluent COD exhibited significant correlation to the microbial community according to the Monte Carlo permutation test analysis (p < 0.05). The abundance of Nitrospira, uncultured Nitrosomonadaceae and Denitratisoma presented strong positive correlations with the influent/effluent concentration of COD and ammonium nitrogen, while Dechloromonas, Thauera, Rhodocyclaceae (norank) and Comamonadaceae (norank) showed positive correlations with water volume and temperature. The established relationship between microbial community and environmental variables in different biologically functional zones of the six representative WWTPs at different geographical locations made the present work of potential use for evaluation of practical wastewater treatment processes.

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China

Gut microbes of animals play critical roles in processes such as digestion and immunity. Therefore, identifying gut microbes will shed light on understanding the annual life of animal species, particularly those that are threatened or endangered. In the present study, we conducted nucleotide sequence analyses of the 16S rRNA genes of gut microbiome of the hooded cranes (Grus monacha) wintering at Shengjin Lake, China, by Illumina high‐throughput sequencing technology. We acquired 503,398 high‐quality sequences and 785 operational taxonomic units (OTUs) from 15 fecal samples from different cranes, representing 22 phyla that were dominated by Firmicutes, Proteobacteria, and Actinobacteria. A total of 305 genera were identified that were dominated by Clostridium, Lysinibacillus, and Enterobacter. The core gut microbiome comprised 26 genera, including many probiotic species such as Clostridium, Bacillus, Cellulosilyticum, and Cellulomonas that could catabolize cellulose. The findings reported here contribute to our knowledge of the microbiology of hooded cranes and will likely advance efforts to protect waterbirds that inhabit Shengjin Lake Reserve during winter.

Identification of novel and differentially expressed MicroRNAs in goat enzootic nasal adenocarcinoma

Background

MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in goats and sheep by enzootic nasal tumor virus (ENTV), is a chronic, progressive, contact transmitted disease.

Methods

In this work, small RNA Illumina high-throughput sequencing was used to construct a goat nasal miRNA library. This study aimed to identify novel and differentially expressed miRNAs in the tumor and para-carcinoma nasal tissues of Nanjiang yellow goats with ENA.

Results

Four hundred six known miRNAs and 29 novel miRNAs were identified. A total of 116 miRNAs were significantly differentially expressed in para-carcinoma nasal tissues and ENA (54 downregulated; 60 upregulated; two only expressed in control group); Target gene prediction and functional analysis revealed that 6176 non-redundancy target genes, 1792 significant GO and 97 significant KEGG pathway for 121 miRNAs (116 significant expression miRNAs and five star sequence) were predicted. GO and KEGG pathway analysis revealed the majority of target genes in ENA are involved in cell proliferation, signal transduction and other processes associated with cancer.

Conclusions

This is the first large-scale identification of miRNAs in Capra hircus ENA and provides a theoretical basis for investigating the complicated miRNA-mediated regulatory networks involved in the pathogenesis and progression of ENA.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3238-5) contains supplementary material, which is available to authorized users.

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome-Picea glauca system at an arctic treeline ecotone

Plant-associated mycobiomes in extreme habitats are understudied and poorly understood. We analysed Illumina-generated ITS1 sequences from the needle mycobiome of white spruce (Picea glauca) at the northern treeline in Alaska (USA). Sequences were obtained from the same DNA that was used for tree genotyping. In the present study, fungal metabarcoding and tree microsatellite data were compared for the first time. In general, neighbouring trees shared more fungal taxa with each other than trees growing in further distance. Mycobiomes correlated strongly with phenological host traits and local habitat characteristics contrasting a dense forest stand with an open treeline site. Genetic similarity between trees did not influence fungal composition and no significant correlation existed between needle mycobiome and tree genotype. Our results suggest the pronounced influence of local habitat conditions and phenotypic tree traits on needle-inhabiting fungi. By contrast, the tree genetic identity cannot be benchmarked as a dominant driver for needle-inhabiting mycobiomes, at least not for white spruce in this extreme environment.

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing

The characterization of bacterial community compositions and the change in perfluoroalkyl acids (PFAAs) along a natural river distribution system were explored in the present study. Illumina high-throughput sequencing was used to explore bacterial community diversity and structure in sediment polluted by PFAAs from the Xiaoqing River, the area with concentrated fluorochemical facilities in China. The concentration of PFAAs was in the range of 8.44-465.60 ng/g dry weight (dw) in sediment. Perfluorooctanoic acid (PFOA) was the dominant PFAA in all samples, which accounted for 94.2 % of total PFAAs. High-level PFOA could lead to an obvious increase in relative abundance of Proteobacteria, ε-Proteobacteria, Thiobacillus, and Sulfurimonas and the decrease in relative abundance of other bacteria. Redundancy analysis revealed that PFOA played an important role in the formation of bacterial community, and PFOA at higher concentration could reduce the diversity of bacterial community. When the concentration of PFOA was below 100 ng/g dw in sediment, no significant effect on microbial community structure was observed. Thiobacillus and Sulfurimonas were positively correlated with the concentration of PFOA, suggesting that both genera were resistant to PFOA contamination.

The complete mitochondrial genome of the white-browed laughingthrush Garrulax sannio (Passeriformes: Leiothrichidae)

The complete mitochondrial genome of the white-browed laughingthrush Garrulax sannio was assembled using next-generation sequencing (NGS) technology. The double-stranded circular genome is 17 848 bp in length, including 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and 2 putative control region. All PCGs are initiated with the ATG codon except for COX1 with GTG as its start codon. Five distinct types of stop codons are present, i.e., AGA (ND5), AGG (COX1 and ND1), TAA (ATP6, ATP8, COX2, CYTB, and ND4L), TAG (ND6), and the incomplete codon T/TA (COX3, ND2, ND3, and ND4). The nucleotide composition is moderately asymmetric (28.94% A, 32.82% C, 15.00% G, and 23.24% T) with an overall GC content of 47.82% ("light strand"). Phylogenetic analysis indicated a close genetic relationship between this species and its congeners G. perspicillatus, G. cineraceus, and G. canorus.

Performance and microbial community dynamics in bioaugmented aerated filter reactor treating with coking wastewater

In this study, zeolite-biological aerated filters (Z-BAFs) bioaugmented by free and magnetically immobilized cells of Arthrobacter sp. W1 were designed to treat coking wastewater containing high concentrations of phenol and naphthalene along with carbazole (CA), dibenzofuran (DBF), and dibenzothiophene (DBT). All treatments were carried out for a period of 100days and the data indicated that bioaugmented Z-BAFs with magnetically immobilized cells was most efficient for treating coking wastewaters. Illumina high-throughput sequencing was used to reveal the microbial community structures of Z-BAFs. Both bioaugmentation treatments could accelerate the shift of the bacterial community structures. The introduced strain W1 remained dominant in the bioaugmented Z-BAFs with magnetically immobilized cells, indicating both strain W1 and the indigenous degrading bacteria played the most significant role in the treatment. Overall, bioaugmented Z-BAF with magnetically immobilized cells can be used to efficiently degrade phenol, naphthalene, CA, DBF, and DBT in coking wastewater.

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing

In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs.

Response of forest soil euglyphid testate amoebae (Rhizaria: Cercozoa) to pig cadavers assessed by high-throughput sequencing

Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro-environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.