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The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems, altering the structure and function of river ecosystems. Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems, but generally convey little information regarding ecosystem functions. In this study, using Illumina MiSeq sequencing technology based on the 16S rRNA gene, river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed. The results show that the total organic carbon (TOC) content was highest at the YZS site (animal husbandry sewage) among the assayed sites, but the species richness and uniformity were lowest at this site, which may have been caused by the high nutrient source of the sewage. Furthermore, in the three YZS samples affected by the long-term discharge of aquaculture tail-water, the unique genus Dechloromonas and the genus Candidatus-Competitor were observed, which are strongly correlated with phosphorus conversion. The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments. According to the PICRUSt functional prediction, the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions, exhibiting richness of functions. Overall, our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities, which is beneficial for the management of river environments. Image, graphical abstract [ABSTRACT FROM AUTHOR]

The host-associated gut microbiota is considered critical for the occurrence and progression of colorectal cancer (CRC); however, systematic evaluations of the changes in the biodiversity and richness of mucosa-associated gut microbiota with the development of CRC have been limited. Twenty-three paired samples from colorectal tumor sites and the surrounding non-tumor tissues were collected from stage I to IV CRC patients. The microbial compositions of the samples were analyzed by Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene. Gut bacterial alterations at the tumor sites and surrounding healthy tissue sites collected from the different stages of CRC patients were analyzed. No significant differences were observed in the overall microbial richness and biodiversity between the CRC tissue and surrounding non-CRC tissue samples, however, composition and community segregation of the gut microbiota with the progression of CRC were observed. A general increasing trend of Bacteroidetes, Firmicutes, and Fusobacteria and decreasing trend of Proteobacteria were observed at the phylum level with the development of CRC. Further analysis revealed that thirty-four taxa differed significantly with the progression of CRC. Conclusively, our findings provide a comprehensive view of the human mucosa-associated gut microbiota, in association with the different stages of CRC. [ABSTRACT FROM AUTHOR]

Soil salinity, poor soil structure and macronutrient deficiencies are three important limitations responsible for poor crop yields in coastal saline soil. Therefore, the objective was to investigate the integrated effects of humic acid fertilizer and vermicompost on maize growth and nutrient uptake in coastal saline soil. The experiment included three treatments: (1) control without humic acid fertilizer and vermicompost (CK); (2) treatment with humic acid fertilizer (H); (3) treatment with vermicompost (V). Soil salinity, aggregates, nutrient availability and uptake, the soil microbial community from next-generation high-throughput sequencing, maize biomass and yield were determined in this study. The results showed that humic acid fertilizer and vermicompost increased soil macroaggregates by 77.59–125.58% and 35.02–91.02%, respectively, which could efficiently decrease soil salinity. Proteobacteria , Actinobacteria and Acidobacteria were the dominant bacterial phyla, and Ascomycota was the dominant fungal phylum in this coastal saline soil. The humic acid fertilizer and vermicompost could affect the fungal community structure in the six-leaf stage (6S) and the bacterial community structure in the harvest stage (HS), which consequently improved soil nutrient availability and maize nutrient uptake. The humic acid fertilizer and vermicompost could enhance nitrogen (N) nutrient absorption of the maize plant in the vegetative growth period (6S) and the phosphorus (P) and potassium (K) nutrient absorption in the reproductive growth period (tasseling stage (TS) and harvest stage (HS)) of maize, which played an important role in increasing the maize yield in coastal saline soil. Therefore, the application of humic acid fertilizer and vermicompost can be integrated as a practice for improving coastal saline soil. • Vermicompost (V) and humic acid fertilizer (H) increased macroaggregates in saline soil. • Soil bacterial and fungal community were improved by V and H in coastal saline area. • Impact of V and H on soil nutrient availability by regulating microbial community. • Integrated amelioration of saline soil by V and H could improve maize nutrient uptake. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal (AM) fungi in both soil and roots were examined in May (summer) and December (winter) under a 4-y drought experiment in a Chinese subtropical secondary forest. Drought significantly decreased AM fungal extra-radical hyphal density, spore density, and root colonization rate in both seasons. These AM parameters were significantly higher in summer than in winter in the control treatment, but only AM fungal extra-radical hyphal density exhibited the same seasonal trend in the drought treatment. In total, 45 AM fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level using Illumina sequencing of 18S rDNA. Drought and season had no significant effects on AM fungal OTU richness in soil and roots. AM fungal community composition in soil and roots was significantly affected by season but not by drought. This finding enhances our understanding of the response of AM fungi to global climate change in subtropical forest ecosystems. • AM fungal abundance was decreased by drought in both seasons. • AM fungal richness was not affected by drought or season. • AM fungal community composition was influenced by season but not by drought. [ABSTRACT FROM AUTHOR]

• Ascomycota and Basidiomycota are the dominant phyla in Panax ginseng -growing soil. • Changes induced by all treatments on soil fungal communities are evaluated. • Adding different leaf litter alters the composition of fungal community. • Basidiomycota were negatively affected by total nitrogen. • Some active biomarkers may be involved in the decomposition of different leaf litters. Soil fungi communities play a vital role in the plant-soil ecosystem and affect plant growth and health, but the underlying mechanism controlling soil fungi communities in understory wild ginseng soil is still unknown. To study that mechanism, a pot culture experiment adding different leaf litters based on a completely randomized design was carried out. The results indicated that 1990 operational taxonomic units were obtained from eighteen samples. Ascomycota and Basidiomycota, the two dominant phyla, accounted for 84.57% of the total valid reads at the phylum level. The observed species and Chao 1 index in treatment E were significantly lower than those in the other treatments, although no significant differences were found among the Shannon index of all treatments (p > 0.05). Different types of leaf litter significantly changed the fungal community composition; specifically, Ascomycota was higher in broad leaf litter treatments (A, C, D and E) than in the coniferous leaf litter treatment (B), but Basidiomycota showed the opposite trend, indicating that Ascomycota and Basidiomycota could be used to identify the species of coniferous and broad leaves. The active biomarker fungal (Bmf), 36 different phylotypes, were identified by a linear discriminant analysis effect size algorithm in all treatments, and some Bmf may participate in the decomposition of different tree litters. Additionally, the changes in fungal community diversity and composition were closely related to the changes in soil microbial biomass carbon, total nitrogen and available phosphorus in all treatment soils. Overall, our study indicated that leaf litter changed the soil fungal community structure, and some Bmf were directly involved in leaf litter decomposition. Bmf is more indicative and helpful for distinguishing leaf species. [ABSTRACT FROM AUTHOR]

Biochar (BC) addition is widely used in agriculture to condition soils. However, the effects of BC addition on soil microbial community diversity and composition in karstic regions are unclear, especially after long-term application. To address this knowledge-gap, a field experiment was established to examine changes in soil physicochemical properties and microbial communities following six years of BC amendment. BC was applied to calcareous soils in a karstic region of southwestern China at four levels (w/w): 0%, 1.0%, 5.0%, and 10%. Bacterial community composition was then investigated in both the rhizosphere and bulk soils by 16S rRNA gene sequencing on the Illumina MiSeq Platform. BC addition increased soil pH, total carbon (TC), total nitrogen (TN), and total hydrogen (TH) contents in the rhizosphere and bulk soils. In addition, BC amendment was associated with changes in soil bacterial community compositions and diversities, especially at higher BC application levels. The relative abundances of Gemmatimonadetes increased in rhizosphere soils with increasing BC amendment, while those of the Bacteroidetes , Firmicutes , and Cyanobacteria decreased. The relative abundances of Proteobacteria and Chloroflexi increased in bulk soils with increasing BC application levels, while those of the Bacteroidetes and Verrucomicrobia decreased. Canonical correspondence analysis indicated that bacterial community composition was related to soil characteristics including pH, TC, TN, and TH contents in both rhizosphere and bulk soils. Importantly, variations in these soil parameters were closely associated with BC application rates. These results indicate that long-term BC application significantly impacts soil bacterial community characteristics in karstic regions via modulation of soil physiochemical properties. • Six years biochar addition altered rhizosphere and bulk soil properties. • Biochar changed the diversity and composition of soil bacterial communities. • Abundance of rhizosphere Gemmatimonadetes was increased by biochar addition. • Biochar increased the abundance of Proteobacteria and Chloroflexi in the bulk soil. • Long-term biochar application significantly affects the bacterial community. [ABSTRACT FROM AUTHOR]

Abstract Overexploitation of rare earth elements (REEs) has caused serious desertification and environmental pollution. The ecological restoration of mining areas has attracted increasing attention in China. Soil microbiota is important for successful ecological remediation of abandoned mine land. In this study, soil samples were collected from a restored REE mine site, and the bacterial community composition and diversity were assessed by Illumina high-throughput sequencing targeting the V3-V4 region of the 16S rRNA gene. Microbiota significantly developed in the remediated land. A total of 663,781 effective 16S rRNA gene sequences were obtained, which were classified into 28 bacterial phyla and 3 archaeal phyla. The dominant phyla across all samples (>5% of total effective sequences) were Proteobacteria , Acidobacteria and Firmicutes. Bacterial diversity indices (OTU number, Shannon index and Chao1 index) of the restored soils were higher than those of the tailings and even surpassed those in the unmined site. Redundancy analysis indicated that soil nutrients (soil organic carbon, available phosphorus and total nitrogen) were the dominant factors, followed by soil pH, affecting bacterial community structure. In general, these results suggested that soil amendment and phytoremediation effectively improved the soil environment of the abandoned mine site, which also increased our understanding of the correlation between microbial variation and soil properties in restored REE mine soils. Graphical abstract Unlabelled Image Highlights • Bacterial community structure was significantly affected by soil amendment and phytoremediation. • Significant increases of bacterial diversity were found in the restored sites. • Organic amendment significantly increased the contents of SOC, TN, TP and AP. • Soil nutrients acted as drivers of bacterial community composition and diversity. [ABSTRACT FROM AUTHOR]

Abstract Despite hostile climate in the Kuwait desert, perennial vegetation patches persist but are affected by anthropogenic pressures and need to be conserved or restored to their original state. Our goal was to assess the bacterial community composition and structure in both rhizospheric and bulk (non-rhizospheric) soil samples from protected and unprotected sites of four dominant terrestrial vegetation types in the Kuwaiti desert. The bacterial composition and structure was investigated by Illumina MiSeq sequencing of the 16S rRNA gene. Compared to other desert soils, a relatively high diversity of bacteria was detected in this study. Bacterial sequences were affiliated with 13 phyla, most abundant of which revealed were Actinobacteria, Proteobacteria, Planctomycetes, Acidobacteria, Bacteroidetes and Firmicutes. The bacterial structure also commonly identified as Chloroflexi, Gemmatimonadetes, Saccharibacteria, Chlamydiae, Armantimonadetes, Deinococcus-Thermus and Verrucomicrobia. The analyses revealed that bacterial communities that were dominated by members of the phyla Actinobacteria and Proteobacteria found with higher diversity indices in rhizospheric soils. In addition, samples with high diversity indices as measured by the Chao1 and invsimpson indices were from rhizospheric soils, with some exceptions. The beta diversity indices of samples/habitats assessed via cluster analysis indicated noticeable differences in the bacterial community compositions of the sites. This study demonstrates the effect of protected and unprotected areas with vegetation covers and anthropogenic disturbances on Kuwait desert soil bacterial communities. This study provides the first insights into bacterial communities associated with protected and unprotected areas across the Kuwait desert. This information is essential for evaluating how natural and anthropogenic drivers affect plant-bacteria-soil systems in the Kuwait desert. Highlights • The study provides the first glimpse of bacterial communities from Kuwait soils. • Bacterial communities affected by site vegetation community and soil protection types. • The study detected thirteen bacterial phyla and a group of unclassified bacteria. • The phyla Actinobacteria and Proteobacteria are the most dominated members observed. [ABSTRACT FROM AUTHOR]

This study investigated the network of polycyclic aromatic hydrocarbon (PAH) degraders in the Yangtze estuarine and coastal areas. Along the estuarine gradients, Proteobacteria and Bacteroidetes were the dominant bacterial phyla, and forty-six potential PAH degraders were identified. The abundance of genes encoding the alpha subunit of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of gram-negative bacteria ranged from 5.5 × 105 to 5.8 × 107 copies g−1, while that of gram-positive bacteria ranged from 1.3 × 105 to 2.0 × 107 copies g−1. The PAH-degraders could represent up to 0.2% of the total bacterial community and mainly respond to PAHs and Cu concentrations, which indicate anthropogenic activities. Salinity and pH showed negative regulating effects on the PAH-degrading potential and the tolerance of bacteria to pollutants. PAH degraders such as Novosphingobium and Mycobacterium exhibit heavy-metal tolerance and core roles in the network of PAH degraders. These outcomes have important implications for bioremediation. Unlabelled Image • Proteobacteria , Bacteroidetes and Chloroflexi persist in contaminated sites. • PAH-degraders represent up to 0.2% of the total bacterial community. • Comamonadaceae , Pseudomonas and Flavobacterium are dominant PAH degraders. • PAHs and metals, salinity, and pH regulated the PAH-degrading potential. • Metal-tolerant Novosphingobium and Mycobacterium are central PAH degraders. [ABSTRACT FROM AUTHOR]

This study investigated the effects of 35 years of application of inorganic fertilizers containing nitrogen (N), phosphate (P), or potassium (K) alone or in combination on the abundance and composition of diazotrophic community in a black soil (Mollisol) in northeast China. The abundance and composition of diazotrophic community were analyzed using qPCR and Illumina MiSeq sequencing targeting nifH genes. Nitrogen fertilization decreased the abundance and Shannon diversity of nifH genes. The diazotrophic community was dominated by Alphaproteobacteria (Bradyrhizobium at the genus level), with relatively higher abundance in the N fertilization treatments than in the non-N fertilization treatments. All diazotrophic communities were clustered into two groups with and without N fertilization history, and the soil pH, total C, total N, and NO 3 −-N significantly influenced the structure of the whole diazotrophic community. Moreover, random matrix theory analysis elucidated a clear difference in network structures between the N and non-N fertilization treatments, with N fertilization causing a less stable network structure. These results highlighted that it was N fertilizer, but not P and K fertilizers, contributed to great changes in the diazotrophic community in this black agricultural soil. [ABSTRACT FROM AUTHOR]

Abstract In this study, a temperature staged anaerobic treatment (TSAT) system featured by thermophilic reactor (R1)-mesophilic reactor (R2) co-digestion was introduced to treat PTA wastewater. The process was successively conducted at three organic loading rates (OLRs): 3.34, 4.45, 6.68 kg COD/(m³·d), respectively (OLRs were R1 basis). The results indicated that TSAT system was highly efficient in PTA wastewater treatment at OLR lower than 4.45 kg COD/(m³·d). Miseq sequencing analysis demonstrated that R1 and R2 were predominated by hydrogenotrophic Methanolinea and acetotrophic Methanosaeta , separately. In addition, TA06 , Caldisericia and Acetothermia associated groups were highly abundant in R1, whereas Chlorobiaceae and Syntrophobacteraceae were largely observed in R2. Tax4Fun analysis suggested that the important functional capabilities were significantly different between R1 and R2 (P < 0.05). The pathways related to aromatic compounds degradation mainly occurred in mesophilic stage, while the biosynthesis and metabolism pathways were more favored in thermophilic stage. Graphical abstract Image 1 Highlights • TSAT system showed excellent capability on PTA wastewater treatment. • Microbiota promoting PTA wastewater treatment were determined in TSAT system. • Enzyme involved in aromatic compounds degradation process were analyzed. • Metabolic characteristics within the TSAT system were evaluated. [ABSTRACT FROM AUTHOR]

Abstract An experimental recirculating aquaculture system was constructed under ambient seawater conditions to compare microbial community diversity of nitrifying and denitrifying biofilters that were derived from a commercial inoculum used for aquarium applications. Next generation sequencing revealed distinct and diverse microbial communities in samples analyzed from the commercial inoculant and the denitrification and nitrification biofilters. In all samples, communities were represented by a few dominant operational taxonomic units (OTUs). Bacteria having the capacity to carry out ammonia and nitrite oxidation were more abundant in the nitrification biofilter. Similarly, the proportion of the bacterial taxa known to carry out heterotrophic and autotrophic denitrification and participate in sulfur cycling were found in the denitrification bioreactor, and likely originated from the ambient environmental water source. Our results indicated that environmental seawater can be a favorable enhancement to the bacterial consortium of recirculating aquaculture systems biofilters. Highlights • Next generation sequencing was performed on populations in a recirculating aquaculture system. • Microbial communities established on biofilters were compared to commercial inoculum. • Environmental seawater used for filling the RAS provided additional bacteria. [ABSTRACT FROM AUTHOR]

Abstract Soil microbial community composition and litter quality are important drivers of litter decomposition, but how litter quality influences the soil microbial composition largely remains unknown. We conducted a microcosm experiment to examine the effects of changes in litter quality induced by long-term N deposition on soil microbial community composition. Mixed-species litter and single-species litter were collected from a field experiment with replicate plots exposed to long-term N-addition in a semiarid grassland in northern China. The litters were decomposed in a standard live soil after which the composition of the microbial community was determined by Illumina MiSeq Sequencing. Changes in litter stoichiometry induced by N-addition increased the diversity of the fungal community. The alpha-diversity of the fungal community was more sensitive to the type of litter (mixed- or single-species) than to the N-addition effects, with higher abundance of fungal OTUs and Shannon-diversity observed in soil with mixed-species litter. Moreover, the relative abundance of saprophytic fungi increased with increasing N-addition rates, which suggests that fungi play an important role in the initial stages of the decomposition process. Litter type and N addition did not significantly change the diversity of bacterial community. The relative abundance of ammonia-oxidizing bacteria was lower in high N-addition treatments than in those with lower N input, indicating that changes in litter stoichiometry could change ecosystem functioning via its effects on bacteria. Our results presented robust evidence for the plant-mediated pathways through which N-deposition affects the soil microbial community and biogeochemical cycling. Highlights • Changes in litter quality increased the diversity of fungal community. • Higher fungal diversity was observed in soil with mixed litter. • Saprophytic fungi increased with increasing N-addition rates. • Ammonia-oxidizing bacteria was lower in high N-addition treatments. [ABSTRACT FROM AUTHOR]

To treat gibberellin (GA) wastewater, a full-scale, multi-stage combined contact process was developed. This whole process employs three anaerobic reactors followed by micro-aerobic, anoxic/aeration and biological oxidation treatment. Pollutant removal results showed that the combined process could remove more than 98% of the chemical oxygen demand (COD), NH 3 N, and SO 4 2− pollutants because of the different microbial communities in each reactor. 16S rRNA gene sequencing was used to examine the microbial communities in the internal circulation (IC) and in the two up flow anaerobic sludge blanket (UASB) reactors, as well as to investigate the effect of sampling elevation on the microbial community. The results showed that Firmicutes and Euryarchaeota were the most dominant phyla at the bacterial and archaeal levels, respectively. High levels of Synergistaceae_uncultured were detected in IC and UASB1. Chloroflexi_uncultured was the dominant genus of bacterial communities within UASB2, and Methanosaeta was the dominant genus of archaeal communities. Principal coordinates analysis (PCoA) revealed variations among the microbial communities in 9 samples, and Venn analysis showed different operational taxonomic units (OTUs) among samples collected at various elevations within the three anaerobic reactors. However, partial Mantel tests indicated no significant correlation between the microbial community structure and elevation in the three anaerobic reactors. [ABSTRACT FROM AUTHOR]

Highlights • Farm manure can increase soil enzymatic activities. • Farm manure can enhance the rhizospheric bacterial abundance and Shannon index. • Bacterial communities correlated with environmental factors and enzymatic activities. • Incorporation of organic manure can improve saline-alkaline soils fertility. Abstract Soil salinization is one of the key factors that threatens plant existence worldwide and is a major challenge to sustain crop production and soil quality. However, there has been limited research on the responses of microbial communities and enzyme activities under soil amendments application in saline alkaline soils. Here, we explored the response of microbial communities and enzyme activities to soil amendments based on 7-year field experiment. The five treatments included FA, amended with farm manure; DE, amended with desulfurization gypsum; SA, amended with sandy soil; M, amended with a mixture of FA, DE and SA; and CK, non-amended control. Relative to the CK treatment, the four amendments, particularly FA, DE and M, significantly decreased the soil pH. Enzyme activities (catalase, urease, alkaline phosphatase and cellulase) were increased in the FA, DE and M treatments, while no difference was observed between SA and CK, except in cellulase. A total of 439,575 effective sequences after filtering out of 1,017,148 raw reads were obtained resulting in 9096 OTUs. Six bacterial phyla of the highest relative abundance were detected including Proteobacteria , Chloroflexi , Bacteroidetes , Actinobacteria , Acidobacteria and Firmicutes across all soil samples (accounting for >85% of the reads). The bacterial community richness was increased in the FA, DE and M treatments, whereas it showed a similar pattern between the CK and SA treatments. Bacterial community diversity was remarkably higher in the M, FA and DE treatments compared to that of CK, while it was reduced in SA. There was a higher similarity in the bacterial communities among DE, FA and M, as well as between CK and SA. Our findings showed that organic manure is a better application approach for the restoration of saline-alkaline soil based on improving the bacterial community and enzyme activities. [ABSTRACT FROM AUTHOR]

Abstract The alpine steppe at Qinghai-Tibetan Plateau is an important area for conserving water source and grassland productivity; however, knowledge about the microbial community structure and function and the risk to human health due to alpine plant-soil ecosystems is limited. Thus, we used prediction methods, such as Tax4Fun, and performed a metagenome pre-study using 16S rRNA sequencing reads for a small scale survey of the microbial communities at degraded alpine steppes (i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), heavily degraded (HD), and extremely degraded (ED) steppes) by Illumina high-throughput sequencing technology. Although there were no significant differences in the microbial alpha diversity among the different degraded alpine steppes and the dominant phyla at the different degraded alpine steppes, including Actinobacteria , Proteobacterial , Acidobacteria and Chloroflexi , were similar, the beta-diversity significantly differed, indicating that alpine steppe degradation might result in variation in microbial community compositions. The linear discriminate analysis (LDA) effect size (LEfSe) analysis found twenty-one biomarkers, most of which belonged to Actinobacteria , suggesting that microbes with a special function (such as the decomposition soil organic matter) might survive in alpine steppes. In addition, the functional profiles of the bacterial populations revealed an association with many human diseases, including infectious diseases. In addition, the microbial communities were mainly correlated with the populations of Gramineae and soil total phosphorous. These results suggested that alpine steppe degradation could result in variations in the microbial community composition, structure and function at Qinghai-Tibetan Plateau. Further studies investigating the degraded alpine steppe environment are needed to isolate these potential pathogenic microbes and help protect livestock using these alpine steppes. Graphical abstract Unlabelled Image Highlights • We investigated the soil microbial communities in degraded alpine steppe using 16S rRNA. • There were no differences in the α-diversity of the microbes in the degraded alpine steppe. • The microbial community structures significantly differed along with the alpine steppe degradation. • The microbial community diversity and abundance were mainly affected by the Gramineae coverage and soil total phosphorous. • The potential function profiling discovered human disease pathways involved in degraded alpine steppe. [ABSTRACT FROM AUTHOR]

Abstract Although effects of biochar application on soil microorganism have been increasingly reported, the direct evidences for demonstrating the contributions of biochar chemical and physical properties to soil microorganisms are still lacking. Herein, we partitioned corn-straw biochar (BC) into three fractions, including aqueous extractable substances (AE), organic extractable substances (OE) and the remaining solid (EBC) after these two extractions. These fractions and BC were added to purple soil for a 30-day incubation. Soil properties, microbial α-diversity indices and microbial community compositions were analysed after the incubation. The results showed the obvious changes in soil properties, along with higher available P, available K and total organic C, as well as, lower pH and available N than those of soil without biochar, were observed in the BC-treated soil. Illumina Miseq sequencing displayed a distinct difference between responses of bacteria and fungi to biochar application, in which fungal richness and diversity were increased, and no significant changes happened in bacterial richness. Furthermore, biochar had apparent effects on bacterial and fungal community compositions at phylum level, which were most close to the influences of AE and EBC, respectively. These results suggested that AE, improving soil nutrients (e.g., total N), played a pivotal role in changing bacterial phylum community composition. The EBC, regarded as physical structure and relatively recalcitrant compounds of BC, had a dominant contribution to the influence of biochar on the fungal community composition. Graphical abstract Unlabelled Image Highlights • Corn-straw biochar (BC) influenced purple soil properties during 1-month incubation. • The α-diversity indices of soil fungi were reduced by BC. • Bacterial and fungal community composition at phylum level was changed by BC. • Aqueous-extractable substance of BC is key factor of changing bacterial community. • Physical structure and recalcitrant C of BC is key role in changing fungal community. [ABSTRACT FROM AUTHOR]

Highlights • Microbial communities were compared in root-rot diseased and healthy soils of Torreya grandis. • Prolonged root-rot infestation decreased tree vitality and soil microbial biomass. • Some fungal taxa (Gibberella and Cryptococcus) were linked with the diseased soil. • Microbial function changes towards a higher C utilization potential in diseased soil. Abstract Soil microorganisms have a profound influence on plant growth, but as well on plant disease. It is still not clear, however, how microbial community structures and functional activities are changing in transitions between healthy and diseased soils. We performed detailed bacterial and fungal community analysis in healthy and root-rot diseased soils of Torreya grandis plantation forest in the subtropical region of China. Soil enzyme activities and microbial metabolic profiling was done to find their interactions with the diseased plants and the microbial functioning. The diseased trees showed lower root biomass, total chlorophyll and N contents in leaf, but higher peroxidase activity. The soils under diseased trees had lower soil organic carbon (SOC) content, but higher pH, moisture and available N content. The microbial diversity was unchanged between the healthy and diseased soils, but the diseased soils had lower 16S rRNA and ITS gene copy numbers. Illumina MiSeq sequencing showed that the fungal rather than the bacterial community composition differed significantly (P < 0.05) and Gibberella and Cryptococcus were associated with the diseased trees. The activities of β-D-cellobiosidase, β-glucosidase and peroxidase and microbial carbohydrate utilization rates were typically enhanced in the diseased soils. Changes in SOC, available N and soil moisture associated to root-rot disease were key factors shaping microbial community composition and activity, and closely linked to plant biomass. Our study showed that prolonged root-rot infestation decreased tree vitality and soil microbial biomass, changed fungal community composition and soil functioning towards a faster organic C decomposition, which potentially may increase soil organic matter turnover. [ABSTRACT FROM AUTHOR]

Abstract This study compared the biohydrogen generation by sub-tropical mixed and pure cultures from the crude glycerol from the biodiesel production using waste cooking oils (WCO). The crude glycerol was pretreated by pH adjustment. The mixed culture was obtained from a subtropical granular sludge of the UASB (Upflow Anaerobic Sludge Blanket) reactor used in the treatment of vinasse from sugarcane of ethanol and sugar industry. It was heat treated in order to inactivate hydrogen-consuming bacteria, which was identified by Illumina MiSeq Sequencing with a relative abundance of 97.96% Firmicutes Philum, 91.81% Clostridia Class and 91.81% Clostridiales Order. The pure culture was isolated from a sub-tropical granular sludge from UASB reactor of treating brewery wastewater and identified as Enterobacter sp. (KP893397). Two assays were carried in anaerobic batch reactors in order to verify the hydrogen production from crude glycerol bioconversion with: (I) mixed culture and (II) pure culture. The experiments were conducted at 37 °C, initial pH of 5.5 for assay I and 7.0 for assay II, with 20 g COD L−1 of crude glycerol. The crude glycerol consumption was 56.2% and 88.0% for the assay I and II, respectively. The hydrogen yields were 0.80 moL H 2 mol−1 glycerol for the assay I and 0.13 moL H 2 mol−1 glycerol for the assay II. Enterobacter sp. preferred the reductive metabolic route, generating 1460.0 mg L−1 of 1,3-propanediol, and it showed to be more sensitive in the presence of methanol from crude glycerol than mixed culture that preferred the oxidative metabolic route with biohydrogen generation. The mixed culture was more able to generate H 2 than pure culture from the crude glycerol coming from the biodiesel production using WCO. Highlights • Crude Glycerol (CG) from biodiesel generation from waste cooking oils. • Identification of Clostridium sp. in mixed culture by Illumina MiSeq Sequencing. • Clostridium sp. degrades crude glycerol via oxidative pathway. • Enterobacter sp. degrades crude glycerol to 1,3-PD via reductive pathway. • Higher H2 yield during CG consumption with Clostridium sp. than Enterobacter sp. [ABSTRACT FROM AUTHOR]

Mixed soil microbiomes were established by introducing aliquots of a paddy soil into a red soil. The new mixed microbiomes effectively metabolized high-molecular-weight polycyclic aromatic hydrocarbons (PAHs, pyrene) in the soil mixtures. The pyrene removal efficiencies were 19% and 98%, respectively, in the original red soil and the paddy soil. The pyrene removal effectiveness by the mixed microbial community was enhanced by increasing the amount of paddy soil inoculant and the pyrene removal rates were 93%, 58% and 27% in paddy soil/red soil mixtures of 1:1, 3:7 and 1:9 (w/w), respectively. Supplementation with sterile paddy soil and nutrients changed the soil environment but the pyrene removal efficiency was not enhanced, indicating that the microbial composition largely determined the extent of pyrene removal. Moreover, the pyrene removal rate was positively related to the pyrene dioxygenase gene ( nidA ) abundance. The greater the percentage of the paddy soil in the soil mixture the greater the similarity of the mixed microbiome to that of the original paddy soil itself. The community of the inoculated sterile paddy soil was similar to that of the red soil and the community diverged from those of the red soil and the paddy soil with increasing culture time. After culture for 42 days, some enriched genera were responsible for PAH degradation, notably Nevskia , Ralstonia , Gemmatimonas and Lysobacter , while some genera have no clear classification information or category name at the genus level, such as f__Acidobacteriaceae and o__JG30-KF-AS9. This study is very important in recognizing the role of natural soil in the formation of a mixed microbiome to stimulate the degradation of PAHs in a soil with low intrinsic PAH degradation capability. [ABSTRACT FROM AUTHOR]

The objective of this study was to characterize the diversity and dynamics of rhizosphere bacterial community, especially the response of dominant and rare bacterial taxa to the cultivation of Bt cotton for different root environments at different growth stages. qPCR analyses indicated that bacterial abundances of the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different at seedling and bolling stages. But no significant differences were detected between the same root zones from Bt and the conventional cotton varieties. Total bacterial genera had similar pattern with dominant genera in abundance, and with rare genera in richness to the changes of bacterial community, respectively. Although the rhizosphere bacterial diversity of the three cotton varieties changed in taproot and lateral root, no significant differences were detected in the same root environments between Bt and conventional cotton. Moreover, Soil pH was more correlated with variations in the bacterial community composition than Bt proteins. In conclusion, these results revealed no indication that rhizosphere bacterial community of Bt cotton had different response to increased Bt protein regarding the same root environment. In particular, dominant and rare bacterial taxa showed the variation in diversity and community composition in different root microhabitats. [ABSTRACT FROM AUTHOR]

Fermented foods may confer several benefits to human health and play an important role in a healthy and balanced diet. Stinky tofu is an important traditional fermented soy product in Asia. In this study, a comprehensive analysis of bacterial diversity in terms of rarefaction abundance, rank abundance, alpha diversity, and principal coordinates analysis was conducted using next-generation sequencing. The results obtained were further verified by culture-dependent methods. In addition, eight biogenic amines were also quantified to determine their levels in stinky tofu during conventional production. Our study revealed that lactobacillus was the major lactic acid bacteria throughout the fermentation process. Further, some potentially harmful bacterial belonging to the genera Halomonas and Solobacterium , were also found existing in the stinky tofu. In case of biogenic amines, the concentration of putrescine, cadaverine and histamine finally increased to high levels while spermine disappeared after the fermentation was completed. After the soaking step, putrescine, tryptamine and β-phenethylamine increased sharply. This work provided an improved understanding of microbes and biogenic amines content associated with the traditionally consumed fermented food. However, there is a need to understand microbial interactions related to biogenic amines during the fermentation, and the origin and survival strategies of two important pathogens detected in our study [ABSTRACT FROM AUTHOR]

Traditional Chinese soybean pastes are homemade using natural fermentation and are quite common and popular in Liaoning Province. In this study, we investigated microbial diversity by collecting 23 samples from 10 cities and sequenced them using 2 × 300 bp Illumina Miseq Sequencing. 16S and ITS primers were used to amplify the V3-V4 region of the bacterial 16S rRNA gene and the ITS1 region of the fungal ITS rDNA gene, respectively. In total, 687,888 filtered bacterial sequences were obtained from nineteen samples and 1,091,649 filtered fungal sequences were obtained from twenty samples. Among the bacterial sequences, Firmicutes (74.77%), Proteobacteria (22.61%), and Actinobacteria (2.55%) were the predominant phyla, with Staphylococcus making up most of the Firmicutes . Among the fungal sequences, Ascomycota , Basidiomycota and Zygomycota accounted for 94.88%, 3.29% and 1.77%, respectively, while Glomeromycota and Chytridiomycota accounted for the remaining 0.06%. Most of the species from Ascomycota were unclassified Trichocomaceae and Debaryomyces , including 404578 and 187827 sequences, respectively. The microbial community in each sample was unique, most likely due to the geographical differences and external factors including the environment and manufacturing process during the fermentation. Soybean paste is the result of fermentation involving a great diversity of microorganisms, which include not only bacteria but also fungi. [ABSTRACT FROM AUTHOR]

Elevated atmosphere CO 2 (eCO 2 ) levels lead to changes in the quantity and composition of rhizodeposition of soybeans. Previously, a majority of studies have focused on the bacterial community response to the eCO 2 in the rhizosphere of soybean with little information regarding the quantitative and compositional changes in the fungal community available. To provide insight into the fungal community response, next generation sequencing of the internal transcribed spacer (ITS) region was conducted for in-depth analysis of changes in fungal abundance and diversity in response to eCO 2 . Four soybean cultivars (i.e. Xiaohuangjin, Suinong 8, Suinong 14 and Heinong 45) were grown for 65 days under ambient CO 2 (aCO 2 ) (390 ppm) and eCO 2 (550 ppm) in Mollisol soils. Elevated CO 2 significantly increased ITS copy numbers in the rhizosphere of the soybean cultivars except Xiaohuangjin and Suinong 14. Principal coordinate analysis (PCoA) revealed that eCO 2 , rather than soybean cultivars, altered the composition of soil fungal communities. Network analysis indicated that eCO 2 simplified the network structure by changing topological roles of operational taxonomic units (OTUs) and key fungal members, which were likely regulated by concentrations of NH 4 + -N, NO 3 − -N and available K and microbial biomass C under eCO 2 . [ABSTRACT FROM AUTHOR]

In order to explore whether the acidogenic phase and methanogenic phase could be separated vertically into a single-stage anaerobic reactor, a controlled double circulation (CDC) anaerobic reactor was proposed for treating traditional Chinese medicine (TCM) wastewater in this study. The results showed that most of the organic pollutants and refractory were removed in the first reaction area where most of the amount of sludge existed. The organic acids were accumulated in the first reaction area, and larger specific methanogenic activity (SMA) and coenzyme F 420 values were found in the second reaction area. Bacterial and archaeal community structures in the two reaction areas of the CDC reactor were analyzed by Illumina MiSeq Sequencing, which revealed that the archaeal community showed larger difference compared with the bacterial community. Differences in the performance and microbial composition of the two reaction areas confirmed that phase separation was implemented in the CDC reactor. [ABSTRACT FROM AUTHOR]

Tiantishan Grottoes, a famous site well known for its historical status in the spread of Buddhism art in ancient China, were selected for a comparison and analysis of microbial taxonomic characteristics on the wall paintings under different preservation conditions: in situ and ex situ conservation. A total of 12 samples were collected from three different cave wall paintings preserved in situ or ex situ . The 16/18S rRNA gene-based sequences revealed a high bacterial diversity and a relative low fungal abundance, including bacterial groups Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Acidobacteria, Deinococcus-Thermus and Fusobacteria; and fungal groups Ascomycota and Basidiomycota. Among them, two bacterial genera of the Promicromonospora and Planomicrobium and fungal order of the Sordariales and the family of Trichocomaceae were dominant in the samples preserved ex situ . Some of them have been reported at other cultural heritage sites and associated with the biodeterioration of cultural relics. The over-growth of these microbes led to the abundant filaments formed visible on the surface of the ex situ wall paintings, which preserved under museum conditions. Application of preservation materials including animal glue and wet gypsum to take them off from grottoes and strengthen, and subsequent long-term preservation under poor conditions in museums were mainly responsible for the microbial outbreaks. To avoid similar problems in the future, reasonable intervention measures and strict micro-environmental control must be implemented to the ex situ preservation of wall paintings. Our results have profound significance for clarify the occurrence of microbial invasions and mechanisms on the wall paintings; it is helpful to development a reasonable artificial intervention measures for conservation work of the wall paintings in the future. [ABSTRACT FROM AUTHOR]

In present study, a hydrolysis acidification (HA) reactor was used for simulated dyeing wastewater treatment. Co-substrates included starch, glucose, sucrose, yeast extract (YE) and peptone were fed sequentially into the HA reactor to enhance the HA process effects. The performance of the HA reactor and the microbial community structure in HA process were investigated under different co-substrates conditions. Results showed that different co-substrates had different influences on the performance of HA reactor. The highest decolorization (50.64%) and COD removal rate (60.73%) of the HA reactor were obtained when sucrose was as the co-substrate. And it found that carbon co-substrates starch, glucose and sucrose exhibited better decolorization and higher COD removal efficiency of the HA reactor than the nitrogen co-substrates YE and peptone. Microbial community structure in the HA process was analyzed by Illumina MiSeq sequencing. Results revealed different co-substrates had different influences on the community structure and microbial diversity in HA process. It was considered that sucrose could enrich the species such as Raoultella , Desulfovibrio , Tolumonas , Clostridium , which might be capable of degrading the dyes. Sucrose was considered to be the best co-substrate of enhancing the HA reactor’s performance in this study. This work would provide deep insight into the influence of many different co-substrates on HA reactor performance and microbial communities in HA process. [ABSTRACT FROM AUTHOR]

Rhizosphere microorganisms contribute to the health and development of crops and these beneficial microbes are recruited to the root-zone when plants experience biotic/abiotic stress. The subterranean pests Holotrichia parallela cause severe crop loss in peanut ( Arachis hypogaea  L.) fields. Hypothesizing that infestation by H. parallela larva may influence the composition of rhizosphere microbial communities, deep sequencing of V3 and V4 hypervariable regions of 16S rRNA gene was used to characterize the rhizosphere bacteria of infested and uninfested peanuts. A total of 2,673,656 reads were generated and an average of 2558 OTUs were obtained for each sample. Comparisons of rhizosphere bacterial community structure of peanuts with those infested by H. parallela larva revealed that the relative abundance of Proteobacteria and Bacteroidetes increased, while that of Actinobacteria decreased in the rhizosphere with infestation. A significant shift in bacterial communities was observed within 24 h after infestation by principal coordinate analysis. For the 332 genera identified in 24 h treatment, infestation of white grubs led to the significant changes of abundance of 67 genera. An increase in the Pseudomonas genus of infested-samples for 24 h was verified by real-time qPCR. Our results indicate H. parallela larvae infestation can quickly leads to the change of peanut rhizosphere microbiome and enrichment of specific bacterial species. But the effects were not persistent. This study provides the insight into the function of rhizosphere microbiome in the interaction between subterranean pests and crops. [ABSTRACT FROM AUTHOR]

This study aims to explore the water quality of dental unit waterlines (DUWLs) and the diversity of microbial communities in DUWLs. Water samples from 33 dental chair units (DCUs) were collected, diluted and then spread on sterilized R2A plate for incubation. Subsequently, the microbial colony-forming units per milliliter (CFU/ml) were recorded by an automatic colony analyzer. Total DNA extracted from the rest of the samples was tested on the Illumina MiSeq PE300 platform. T-test and Kruskal–Wallis rank test were adopted for statistical analysis. Significance was assumed at a P < 0.05. After incubation, the average total microbial count was 21,413.13 ± 17,861.00 CFU/ml. High-throughput sequencing revealed 10 bacterial phyla, including 9 identified and 1 unclassified phyla. Totally 63 sequences were identified at the genus level, including 42 genera, 3 tentative species and 18 unclassified genera. In addition, 7 potential human pathogenic bacteria were detected. In summary, department, brand and service life of DCUs do not influence the water quality of DUWLs significantly. The diversity of microbial communities in DUWLs is abundant and includes both pathogenic and some unknown bacteria. [ABSTRACT FROM AUTHOR]

This study focused on comparing bacterial communities from two lab-scale sequencing batch reactors (SBR) operated in nitritation and nitratation mode, respectively. Four samples were collected until the bioreactors had been run at a stable and efficient nitrogen conversion at different operational temperatures of 22 °C and 12 °C. The bacterial community compositions were profiled by Illumina MiSeq sequencing and quantitative real-time (q-PCR). Sequencing results indicated that bacterial compositions in the two reactors at the phylum level showed a similar structure with the decreased temperature, while the disparity between respective heterotrophic communities was clearly demonstrated at the genus level except autotrophic nitrogen-oxidizing species, Nitrosomonas and Nitrobacter highly enriched inside the bioreactors. In addition, the dominated Nitrosomonas and Nitrobacter were further checked through q-PCR and high concentration heterotrophic denitrifiers using nirK as gene markers were also found, consistent with a variety of potential heterotrophs analyzed by high-throughput sequencing. Due to the weak effect of temperature on bacterial communities of different functional nitrifying sludge, heterotrophic communities possibly depended on the influent substrate. Taking into account these results, heterotrophic bacterial communities coexisting with ammonia-oxidizing bacteria (AOB) or nitrite-oxidizing bacteria (NOB) were mutually different and distinct in the diversity and stability. [ABSTRACT FROM AUTHOR]

Soil microbial communities are important for ecological restoration and succession on mine tailings. In the present study, we performed Illumina sequencing to investigate the effects of long term Lespedeza bicolor revegetation on bacterial diversity and community structure in mine tailings under subtropical and moist climatic conditions. Microbial diversity indices (Shannon, OTU number and coverage estimator) of the revegetated soils were higher than that of the control, and increased over sampling period compared to the decreased pattern in the control. Species within known acid tolerant and nutrient regulated genera dominated both revegetated tailings and the control, and exhibited more abundant in the revegetated tailings. At the phylum level, percentage of the Proteobacteria and Actinobacteria were remarkedly higher in revegetated tailings than that in the control, while Chloroflexi performed reversely. Overall, this study found the positive role of L. bicolor revegetation in bacterial diversity development in the acidic mine tailings. Furthermore, the 30-year L. bicolor revegetation made the microbial community structure more homogenizable as a decrease of dissimilarity in tailings was identified over sampling times. Redundancy analysis at the OTU level indicated that Olsen-P and pH were the main regulators of microbial composition, suggesting that soil P and pH are determinant for ecological restoration and microbial community development in acidic mine tailings. [ABSTRACT FROM AUTHOR]

[Display omitted] 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. [ABSTRACT FROM AUTHOR]

Apart from improving the physical and chemical condition of arable soils, cover crops have the potential to boost and activate selected soil microbiota that could contribute to improved nutrient cycling and strengthened disease suppressiveness. However, a main crop can only benefit from cover crop-induced microbial shifts if these persist until the onset of the main growing season. Here, we map the persistence of microbiome changes by cover crops over time. We performed a field experiment on a sandy soil with ten different cover crop monocultures belonging to five plant families, one cover crop mixture and a fallow control. Cover crops were grown for 4.5 months under field conditions in 70-L bottomless containers in a random block design with eight replications. We studied the total (DNA-based) and the potentially active (RNA-based) microbial fractions at the onset of the main growing season, and just after the harvest of the main crop, potato (respectively 3.5 and 10 months after cover crop termination), through MiSeq sequencing. All cover crops tested induced shifts in the soil microbiome that lasted at least until the onset of the main growing season. Cover crop treatments gave rise to species and even cultivar-specific microbial footprints, and - although roughly the same trends were observed - DNA-based microbial shifts were not necessarily paralleled by similar changes at RNA level. We conclude that cover crops have the potential to act as handles to steer the soil microbiome in a way that is supportive of sustainable crop production. • Cover crop-induced microbial shifts last till the onset of the main growing season. • Further persistence of microbial shifts is cover crop-species dependent. • Cover crop-specific bacterial, fungal and protist footprints were identified. • DNA and RNA-based cover crop microbial footprints are comparable but dissimilar. [ABSTRACT FROM AUTHOR]

Shifts in bacterial community composition and abundance of nitrifiers during aerobic granulation, and the effects of wastewater composition on them were investigated using Illumina sequencing and quantitative PCR. The bacterial diversity decreased sharply during the post-granulation period. Although cultivated with different wastewater types, aerobic granular sludge (AGS) formed with similar bacterial structure. The bacterial structure in AGS was completely different from that of seed sludge. The minor genera in seed sludge, e.g., Arcobacter , Aeromonas , Flavobacterium and Acinetobacter , became the dominant genera in AGS. These genera have the potential to secrete excess extracellular polymer substances. Whereas, the dominant genera in seed sludge were found in less amount or even disappeared in AGS. During aerobic granulation, ammonia-oxidizing archaea were gradually washed-out. While, ammonia-oxidizing bacteria, complete ammonia oxidizers and nitrite-oxidizing bacteria were retained. Overall, in this study, the bacterial genera with low relative abundance in seed sludge are important for aerobic granulation. [ABSTRACT FROM AUTHOR]

As the chemical quality of crop residue is likely to be affected by elevated CO 2 (eCO 2 ), residue amendments may influence soil organic carbon (SOC) sequestration. However, in Mollisols, the dynamics of the SOC fractions in response to amendment with wheat residue produced under eCO 2 and the corresponding microbial community composition remain unknown. Such investigation is essential to residue management, which affects the soil quality and productivity of future farming systems. To narrow this knowledge gap, 13 C–labeled shoot and root residue derived from ambient CO 2 (aCO 2 ) or eCO 2 were amended into Mollisols and incubated for 200 days. The soil was sampled during the incubation period to determine the residue-C retained in the three SOC fractions, i.e., coarse intra-aggregate particulate organic C (coarse iPOC), fine iPOC and mineral-associated organic C (MOC). The soil bacterial community was assessed using a MiSeq sequencing instrument. The results showed that the increase in SOC concentrations attributable to the application of the wheat residue primarily occurred in the coarse iPOC fraction. Compared with the aCO 2 -derived shoot residue, the amendment of eCO 2 -derived shoot residue resulted in greater SOC concentrations, whereas no significant differences ( P > 0.05) were observed between the aCO 2 - and eCO 2 -derived roots. Principal coordinates analysis (PCoA) showed that the residue amendment significantly ( P ≤ 0.05) altered the bacterial community composition compared with the non-residue amendment. Additionally, the bacterial community in the aCO 2 -derived shoot treatment differed from those in the other residue treatments until day 200 of the incubation period. The eCO 2 -derived shoot treatment significantly increased ( P ≤ 0.05) the relative abundances of the genera Acidobacteriaceae_(Subgroup_1)_uncultured , Bryobacter , Candidatus_Solibacter , Gemmatimonas and Nitrosomonadaceae_uncultured , whereas the opposite trend was observed in Nonomuraea , Actinomadura , Streptomyces and Arthrobacter ( P ≤ 0.05). These results imply that the response of the microbial community to the eCO 2 -derived shoot treatment is associated with its contribution to the POC fractions. [ABSTRACT FROM AUTHOR]

This study investigated the biological hydrolysis performance at 35 °C (BH35), 42 °C (BH42), and 55 °C (BH55) and the effect of temperatures on microbial communities of the hydrolyzed sludge. The results showed that the suspended solid reduction, volatile fatty acids (VFA) production, and biogas production increased with the BH temperatures. VFAs produced in the sludge BH included acetic acid, propionic acid, isobutyric acid, butyric acid, and isovaleric acid with the fractions of acetic acid increased with BH temperatures. The Illumina MiSeq sequencing analysis showed that the microbial taxonomic structures of the BH systems varied with BH temperatures. It was found that Acidaminobacter at 35 °C, Proteiniphilum and Lutispor at 42 °C, and Gelria at 55 °C were the main protein fermenting bacteria genera, while the carbohydrate fermenting bacteria might belong to the genera of Macellibacteroides and Paludibacter at 35 °C, Fronticella at 42 °C, and Tepidimicrobium at 55 °C. [ABSTRACT FROM AUTHOR]

Soil bacteria play a vital role in terrestrial ecosystems and are very sensitive to changes in the environment. Land subsidence due to underground coal mining could affect soil properties, but the extent of this effect on the soil bacterial community remains unclear. Here, we investigated the effect of land subsidence on soil bacterial communities and their response to changes in the soil environment in a control area and a land subsidence area in the West China Aeolian Sand Area. The results showed that electrical conductivity (EC), total carbon, (TC), total nitrogen (TN), available potassium (AK) and soil organic matter (SOM) at a soil depth of 20 cm were significantly decreased in the land subsidence area compared to the unexploited area, and Illumina MiSeq sequencing data revealed that the bacterial community at a soil depth of 0–180 cm was dominated by Pseudomonas, Gp4, Gp6, Sphingomonas , Gemmatimonas, Arthrobacter , Aciditerrimonas and Gaiella . Land subsidence decreased soil microbial richness and diversity. In addition, there was a significant decrease in the relative abundance of some core genera in the topsoil, such as Sphingomonas, Nocardioides and Saccharibacteria_genera_incertae_sedis , indicating that the dominant bacteria had strong anti-interference abilities and played important roles in the nutrient-poor soils of the mining area. Redundancy analysis (RDA) showed that the main factors driving the changes in the bacterial community structure were EC, water content (WC) and soil depth. The vertical leakage of water and nutrients was caused by subsidence and cracks in the ground, leading to decreased soil microbial richness and diversity. These results suggested that the soil nutrients and soil microbial community has yet to recover by self-healing after two years of land subsidence; thus, artificial restoration might be required. [ABSTRACT FROM AUTHOR]

Despite the continuing development of new insect-derived food products, microbial research on edible insects and insect-based foods is still very limited. The goal of this study was to increase the knowledge on the microbial quality of edible insects by comparing the bacterial community composition of mealworms ( Tenebrio molitor ) and crickets ( Acheta domesticus and Gryllodes sigillatus ) from several production cycles and rearing companies. Remarkable differences in the bacterial community composition were found between different mealworm rearing companies and mealworm production cycles from the same company. In comparison with mealworms, the bacterial community composition of the investigated crickets was more similar among different companies, and was highly similar between both cricket species investigated. Mealworm communities were dominated by Spiroplasma and Erwinia species, while crickets were abundantly colonised by ( Para ) bacteroides species. With respect to food safety, only a few operational taxonomic units could be associated with potential human pathogens such as Cronobacter or spoilage bacteria such as Pseudomonas . In summary, our results implicate that at least for cricket rearing, production cycles of constant and good quality in terms of bacterial composition can be obtained by different rearing companies. For mealworms however, more variation in terms of microbial quality occurs between companies. [ABSTRACT FROM AUTHOR]

In this study, we investigated the effects of four long-term fertilization regimes that were performed over 30 years, namely, non-fertilization (NoF), chemical fertilization (CF), manure fertilization (M) and chemical fertilization plus manure (CFM), on a range of soil properties and fungal communities at three locations which located in the northern, middle and southern parts of the black soil region of northeast China. The fungal communities were primarily analyzed by Illumina MiSeq sequencing targeting fungal rRNA operon ITS1 region. The results showed that the fertilizers (organic or inorganic) generally increased the soil nutrient contents and fungal abundances. Principal coordinate analysis (PCoA) revealed that all fungal communities were separated into three groups according to their sampling locations, and the soil pH was the most influential factor in determining the total fungal communities across the three locations. Similar fertilization treatments had inconsistent influences on the fungal community compositions and the most influential soil factor in shaping fungal community structures varied among the three locations. Amending with inorganic fertilizers increased the relative abundances of potentially pathogenic fungi in the southern location, while the addition of manure suppressed possible pathogenic fungal growth and enhanced the growth of beneficial fungi in the three locations. Our findings highlighted that the influences of geographical separation along with fertilization regimes should be considered when examining the responses of fungal communities to fertilization regimes in agricultural management. [ABSTRACT FROM AUTHOR]

Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition. [ABSTRACT FROM AUTHOR]

Biodegradation of traditional Chinese medicine (TCM) wastewater was investigated in a pilot-scale anaerobic-anoxic-aerobic combined process, which was composed of an expanded granular sludge blanket (EGSB) reactor, a hydrolysis acidification (HA) reactor and a biological contact oxidation (BCO) reactor. In stable stage, the average values of COD and color in the combined process effluent were 45.7 mg L −1 and 13 times, respectively. Excellent linear relations (R 2 > 0.915) were achieved between color and UV 254 at three color levels. Comprehensive community structures of the combined process were analysed by Illumina MiSeq Sequencing, which revealed that microbial community in the aerobic reactor had the greatest diversity and richness. Bacteroidetes , Firmicutes and Proteobacteria were dominant phyla in the three reactors, and Bacteroidales , Geobacter , ZB2 were the predominant functional microorganisms in the anaerobic, anoxic and aerobic reactors, respectively. Good removal efficiencies and presence of core microorganisms confirmed that the combined process was feasible for treating TCM wastewater. [ABSTRACT FROM AUTHOR]

Although biochar amendment has been extensively evaluated as a promising strategy to improve soil quality, most evaluations have been conducted in the laboratory or under short-term field conditions, which restricted us to understand the long-term effects of biochar as a soil amendment. As the residence time of biochar in soils is expected to be hundreds to thousands of years, this study focused on revealing whether biochar addition influences soil physiochemical properties and fungal community composition in a black soil of northeast China over the long term. Biochar was added to the micro-plots at 0%, 2%, 4%, and 8% of the total mass of the top 20 cm of the soil in the spring of 2012, and soil samples were collected seasonally four times in 2014. The results indicate that soil pH, moisture, total C, total N, total P, NO 3 − -N, available K and the C/N ratio significantly increased but soil bulk density and total K content decreased with biochar addition. The soil fungal abundance determined using quantitative real-time PCR showed that the number of fungal ITS gene copies increased with biochar addition. The soil fungal community composition determined using the Illumina MiSeq sequencing method showed that community diversity was not influenced by biochar addition but the community composition was influenced. The impact of biochar on changes in community composition was not reflected at the phylum level, but at the genus and operational taxonomic units (OTU) levels. The relative abundance of Fusarium decreased, but Guehomyces increased with biochar addition over the first three sampling dates. The relative abundances of several OTUs classified as potential crop pathogens decreased with biochar addition, suggesting that biochar amendment may be beneficial in terms of suppressing the occurrence of crop disease over the long term. In addition, canonical correspondence analysis indicated that fungal community composition was associated with soil parameters such as pH, soil moisture, total C, total N, total K and available K. The changes in these soil characteristics were highly correlated with the amounts of biochar addition, suggesting that the impacts of long-term biochar amendment on the soil fungal community occurred indirectly as a result of the alteration of soil physiochemical properties. [ABSTRACT FROM AUTHOR]

Both nitrogen (N) and phosphorus (P) may limit plant production in steppes and affect plant community structure. However, few studies have explored in detail the differences and similarities in the responses of belowground microbial communities to long-term N and P inputs. Using a high-throughput Illumina Miseq sequencing platform, we characterized the bacterial communities in a semi-arid steppe subjected to long-term N or P additions. Our results showed that both the Chao richness and Shannon's diversity were negatively correlated to N input rate, while only Chao richness was significantly and negatively correlated to P input rate. Also, both N and P additions altered the bacterial community structure. The bacterial community between plots of the same N or P input rate was much more dissimilar with the higher input level, indicating more severe niche differentiation in pots with higher N or P input. N Inputs significantly increased the relative abundance of the predicted copiotrophic groups ( Proteobacteria and Firmicutes ) but reduced the predicted oligotrophic groups ( Acidobacteria , Nitrospirae , Chloroflexi ), with the order Rhizobiales being most affected. P additions significantly affected only two phyla (Armatimonadetes and Chlorobi ), which were positively correlated with P source. Results from the structural equation modelling (SEM) showed that N additions affected the bacterial community primarily by changing the pH, while P additions did so mainly by improving P availability. Our results suggest that the below-ground bacterial communities are more sensitive to N inputs, but P inputs can also play an important role in bacterial niche differentiation. These findings improve our understanding of bacterial responses to N and P inputs, and their impacts on bacterial-mediated processes, especially in the context of increasing anthropogenic nutrient inputs. [ABSTRACT FROM AUTHOR]

Characterizing microbial communities associated with disease-suppressive soil is an important first step toward understanding the potential of microbiota to protect crops against plant pathogens. In the present study, we compared microbial communities in suppressive- and conducive-soils associated with Fusarium wilt disease in a vanilla long-term continuous cropping system. Suppressive soil was associated with higher fungal diversity and lower bacterial diversity. The fungal phyla Zygomycota and Basidiomycota , and the bacterial phyla Acidobacteria , Verrucomicrobia , Actinobacteria and Firmicutes were strongly enriched in the suppressive soil. Notably, suppressive soil was dominated by the fungal genus Mortierella , accounting for 37% of the total fungal sequences. The hyper-dominance of Mortierella spp. in suppressive soil suggests that this taxon may serve as an indicator and enhancer of Fusarium wilt disease suppression in vanilla. In addition, Molecular Ecological Network analysis revealed that fungal communities were more connected and showed more co-occurrence relationships in the suppressive versus conducive soils. Our results indicate that fungal communities may be important in the development of soil suppressiveness against vanilla Fusarium wilt disease. [ABSTRACT FROM AUTHOR]

Poplar plantations have been established around the world to provide timber or fuelwood and to control erosion in degraded areas. The objective of this study was to investigate the effects of converting croplands to long-term hybrid poplar ( Populus × euramericana cv. I-72) plantations for 10, 15 and 20 years on soil bacterial and fungal communities and on their relationships with soil organic carbon (SOC) mineralization. Overall, the results indicated that the long-term hybrid poplar plantations increased soil pH, SOC, total N and moisture contents and decreased dissolved organic carbon (DOC), NH 4 + and NO 3 − contents compared to that on the cropland. There were lower cumulative amounts of CO 2 respired and SOC mineralization rates in the hybrid poplar plantation soils compared to that of the cropland. The hybrid poplar plantation with 20 years caused a greater fungal internal transcribed spacer (ITS) gene copy number and a lower bacterial 16S rRNA gene copy number and dehydrogenase and β-glucosidase activities compared to that in the cropland soils. As indicated by Illumina MiSeq sequencing, the establishment of hybrid poplar plantations harbored distinct soil bacterial and fungal communities, which were strongly correlated with specific soil properties. We further found that the SOC mineralization rate was positively correlated to the bacterial abundance and the relative abundances of Actinobacteria and Bacteroidetes, whereas negatively correlated to the fungal abundance. This study suggested that the long-term hybrid poplar plantation reduced SOC mineralization, causing changes in habitats that favor fungal community growth and shifts in bacterial community composition to more facultative and/or obligate anaerobes and less microbes that are capable of decomposing recalcitrant carbon, which may help enhance SOC accumulation in soil and mitigate climate change. [ABSTRACT FROM AUTHOR]

• Day 3 is a turning point for the dynamics of gut bacteria during vermicomposting. • Bacteria dynamics differed in earthworm foregut and hindgut in vermicomposting. • The changes of gut bacteria are related to nutrition supply of compost. • Bacterial structure is stable in the hindgut in the end of vermicomposting. Earthworm gut microbiota is vital in degrading bio-waste during vermicomposting. However, microbial dynamics in earthworm gut during this process are unclear. Thus, the aim is to firstly report the bacterial dynamics in both foregut and hindgut of earthworms over a 28 days' timeframe of vermicomposting by Eisenia foetida with the nutrition supplied by kitchen waste. Results showed that except the changing of the bacterial diversity, composition and structure, dynamics of the foregut and hindgut bacteria also differed during vermicomposting which related to the changes of nutrient provision. Day 3 was a turning point. The abundant bacteria of the top 20 % genera nearly did not overlap between the foregut and hindgut. In the end of vermicomposting, a remarkable stable bacterial structure appeared in the hindgut compared to somewhat muddled one in the foregut. Understanding the dynamics of earthworm gut microbiota enables the improvements to regulate the efficiency of organic waste vermicomposting. [ABSTRACT FROM AUTHOR]

[Display omitted] • PSB addition notably increased available phosphorus from 0.83 to 1.23 g kg−1. • PSB addition significantly increased abundances of phosphorus-cycling genes. • PSB inoculation notably affected compost bacterial community composition. • Stochastic and homogenizing processes affected more on bacterial community assembly. • Rare bacteria potentially mediated organic phosphorus mineralization. Understanding ecological roles of phosphate-solubilizing bacteria (PSB) is important to optimize composting systems. Illumina MiSeq sequencing, gene quantitation, and statistical analyses were employed to explore ecological mechanisms underlying available phosphorus (AP) facilitation during composting with the inoculation of PSB Pseudomonas sp. WWJ-22. Results displayed that the inoculation of PSB significantly increased AP from 0.83 to 1.23 g kg−1, and notably increased abundances of phosphorus-cycling genes as well as numbers of PSB mineralizing phytate and lecithin. The PSB addition significantly affected compost bacterial community composition, and phosphorus factions and phosphorus-cycling genes independently explained 25.4 % and 25.0 % bacterial compositional dissimilarity. Stochastic and homogenizing processes affected more on bacterial community assembly, and rare bacteria potentially mediated organic phosphorus mineralization. These results emphasized that phosphorus fractions, PSB number, phosphorus-cycling gene abundance, and bacterial community composition contributed differently to phosphorus availability. Findings highlight ecological roles of exogenous PSB during chicken manure composting. [ABSTRACT FROM AUTHOR]

Chinese strong-flavor liquor (CSFL) is fermented in cellars lined with pit mud (PM). This PM, specific fermented clay, contains microbes that play important roles in CSFL production. However, there is limited information about fungal community structure and cellar-age-related changes in PM. In this study, PM samples were removed from the cellars used for 5 and 100 years and characterized using denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq sequencing. Both methods revealed there were no significant differences in fungal species diversity (Shannon index, Chao1, and observed species) between the 5- and 100-year PM samples ( p > 0.05), but the communities were more stable in the 100-year PM samples (UPGMA). Illumina MiSeq sequencing allowed identification of 111 fungal genera belonging to 4 phyla (Ascomycota, Zygomycota, Basidiomycota, and Chytridiomycota) in the PM samples, with the predominant phylum being Ascomycota. The results also indicated that the compositions of dominant genera in the PM samples were significantly changed during long-term CSFL fermentation. There were relatively more Rhizopus , Phoma , and Trichosporon in the 5-year PM samples, and Aspergillus and Candida were most highly represented in the 100-year PM samples ( p < 0.05). Of these, Candida increased its relative abundance significantly in the 100-year samples ( p < 0.05). Overall, the results provide novel insights into the fungal community associated with CSFL production, and may suggest why fermentation in a cellar with PM that has been in usage for a longer time allows better quality CSFL production. [ABSTRACT FROM AUTHOR]

Illumina MiSeq high-throughput sequencing was used to reveal the temporal dynamic of microbial community structure and bacterial diversity in an integrated fixed-film activated sludge (IFAS) system over a seven-month period. Microbial community structure and bacterial diversity varied with different months in the system. The biofilm phase showed a more stable microbial community trait compared with the sludge phase with the fall in environmental temperature. Proteobacteria was the most predominant phylum in the IFAS system, followed by Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes and candidate division TM7. The most predominant ammonia oxidizing bacteria and nitrite oxidizing bacteria in the IFAS system were Nitrosomonas and Nitrospira, respectively. An evident shift in the abundance of nitrifying bacteria took place in the biofilm and sludge of the IFAS system during the sampling months. Principal coordinate analysis and a clustered heat map indicated that living conditions and temperature seemed to be the key factors in shaping the microbial community in the IFAS system. [ABSTRACT FROM AUTHOR]