Revealing the anaerobic acclimation of microbial community in a membrane bioreactor for coking wastewater treatment by Illumina Miseq sequencing

The dynamic change of microbial community during sludge acclimation from aerobic to anaerobic in a MBR for coking wastewater treatment was revealed by Illumina Miseq sequencing in this study. The diversity of both Bacteria and Archaea showed an increase–decrease trajectory during acclimation, and exhibited the highest at the domestication interim. Ignavibacteria changed from a tiny minority（less than 1%） to the dominant bacterial group（54.0%） along with acclimation. The relative abundance of Betaproteobacteria kept relatively steady, as in this class some species increased coupled with some other species decreased during acclimation. The dominant Archaea shifted from Halobacteria in initial aerobic sludge to Methanobacteria in the acclimated anaerobic sludge. The dominant bacterial and archaeal groups in different acclimation stages were indigenous microorganisms in the initial sludge, though some of them were very rare. This study supported that the species in＂rare biosphere＂ might eventually become dominant in response to environmental change.

Alterations in the human oral microbiome in cholangiocarcinoma

Dear Editor,Alterations in the human microbiome are closely related to various hepatobiliary diseases.Gut microbial dysbiosis has been found in patients with cholangiocarcinoma(CCA)[1].However,the characteristics of oral microbiome in patients with CCA have not been studied.

不同落叶果树根际微生物群落代谢与组成的差异性研究

【目的】从根际微生物群落代谢与组成方面探讨不同落叶果树根际差异性。【方法】利用Biolog ECO板方法与Illumina Miseq sequencing技术,以未种植果树区域土壤为对照,研究苹果、梨及葡萄等8种落叶果树根际微生物群落的代谢与组成。【结果】8种果树根际微生物的代谢活性与功能多样性指数(除Pielou均匀度指数E外)均显著高于对照。比较8种果树根际微生物群落的碳源利用特征情况发现,杏树根际微生物群落对酚酸类物质(PC,phenolic compounds)的利用比率显著下降,对碳水化合物(CH,carbohydrate)的利用比率显著上升,而对照土壤微生物群落对氨基酸类(AA,amino acids)碳源利用比率最高。细菌与真菌群落纲水平相对丰度表明,8种果树根际细菌与真菌群落相对丰度存在明显差异,其中苹果与核桃γ-变形菌纲相对丰度较其他果树显著上升;而与细菌群落相比,8种果树根际真菌群落在纲水平上差异更为明显。基于纲水平优势菌与微生物群落代谢之间的相关性分析表明,微生物群落代谢与Betaproteobacteria、Alphaproteobacteria及Sphingobacteriia呈显著正相关,而与Gemmatimonadetes、Sordariomycetes、Glomeromycetes及Chytridiomycetes均呈显著负相关。另外,RDA分析表明,微生物功能多样性(除E外)与细菌α多样性呈正相关,而与真菌α多样性呈负相关。【结论】8种果树微生物群落碳代谢存在显著差异。8种果树根际细菌与真菌群落均存在显著差异,而真菌群落较细菌差异更为显著。根际微生物群落代谢与细菌群落呈正相关,而与真菌群落呈负相关。

香蕉秸秆不同还田模式对土壤微生物群落的影响

采用土壤室内培养的方法,以香蕉秸秆不同还田模式为试验唯一变量因素,设置3个处理(无秸秆还田CK;将香蕉秸秆覆盖到土壤表层,作为秸秆自然还田处理F;将土壤与香蕉秸秆彻底混合,作为秸秆掩埋还田处理T),分析香蕉秸秆不同还田模式下的微生物群落差异,以期揭示香蕉秸秆的不同还田模式对土壤微生物的影响。结果表明:T、F处理与CK处理相比,真菌门中Basidiomycota相对丰度分别增加1.3%和2.8%;细菌门中Acidobacteria相对丰度分别增加5.1%和1.1%,Actinobacteria的相对丰度分别增加1.9%和3.2%。处理间Fusarium相对丰度大小顺序为CK>F>T。处理间细菌群落的丰富度(SChao1)和多样性(HShannon)大小顺序均为T>F>CK,真菌群落并无明显差异。聚类分析表明,T处理土壤微生物群落结构与CK处理明显不同。主坐标分析和OTU数量分布结果表明,T处理土壤微生物群落结构与F处理相近。本研究结果显示,T处理增加了土壤细菌群落的丰富性与多样性,改变了土壤微生物的群落结构,同时提高了具有分解功能的微生物分类属的相对丰度,并显著降低了病原菌的相对丰度。

A comprehensive analysis of the response of the fungal community structure to long-term continuous cropping in three typical upland crops

Certain agricultural management practices are known to affect the soil microbial community structure;however,knowledge of the response of the fungal community structure to the long-term continuous cropping and rotation of soybean,maize and wheat in the same agroecosystem is limited.We assessed the fungal abundance,composition and diversity among soybean rotation,maize rotation and wheat rotation systems and among long-term continuous cropping systems of soybean,maize and wheat as the effect of crop types on fungal community structure.We compared these fungal parameters of same crop between long-term crop rotation and continuous cropping systems as the effect of cropping systems on fungal community structure.The fungal abundance and composition were measured by quantitative real-time PCR and Illumina MiSeq sequencing.The results revealed that long-term continuous soybean cropping increased the soil fungal abundance compared with soybean rotation,and the fungal abundance was decreased in long-term continuous maize cropping compared with maize rotation.The long-term continuous soybean cropping also exhibited increased soil fungal diversity.The variation in the fungal community structure among the three crops was greater than that between long-term continuous cropping and rotation cropping.Mortierella,Guehomyces and Alternaria were the most important contributors to the dissimilarity of the fungal communities between the continuous cropping and rotation cropping of soybean,maize and wheat.There were 11 potential pathogen and 11 potential biocontrol fungi identified,and the relative abundance of most of the potential pathogenic fungi increased during the long-term continuous cropping of all three crops.The relative abundance of most biocontrol fungi increased in long-term continuous soybean cropping but decreased in long-term continuous maize and wheat cropping.Our results indicate that the response of the soil fungal community structure to long-term continuous cropping varies based upon crop types.

Comparative population genetic analyses suggest hybrid origin of Rhododendron pubicostatum,an endangered plant species with extremely small populations endemic to Yunnan,China

Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species.In the present study,we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach.Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus.Interestingly,genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh.pubicostatum.This sympatry should be considered a unimodal hybrid zone,since Rh.pubicostatum is predominant here.Unimodal hybrid zones are uncommon in Rhododendron,despite the fact that hybridization frequently occurs in the genus.Issues pertaining to the conservation of Rh.pubicostatum resulting from admixture of genetic material from its parental species are discussed.

Soil Fungal Diversity and Community Composition in Response to Continuous Sweet Potato Cropping Practices

Soil fungi are extremely important for maintaining soil health and plant production in agricultural systems.Currently,the effect of continuous cropping of sweet potato on soil fungal communities and physiochemical parameters has not been well documented.In the present study,four sweet potato fields consecutively monocultured for 1,2,3,and 4 years were selected to investigate the effect of monoculture on soil fungal communities through Illumina MiSeq sequencing.Continuous cropping of sweet potatoes dramatically altered the fungal community composition,whereas fungal diversity was almost unchanged.Ascomycota and Basidiomycota were the most abundant phyla in all soil samples,accounting for 32.59%and 21.14%of the average relative abundance,respectively.The abundance of some potential pathogens,such as Ascobolus spp,specifically Ascobolus stercorarius,and some unknown fungi increased significantly as the sweet potato monoculture period increased,and their presence were highly positively correlated with disease incidence.In contrast,Basidiomycota,Bullera,Fusarium and Trichocladium most likely play roles as antagonists of sweet potato disease development,as their relative abundance decreased significantly over time and were negatively correlated with disease incidence.Redundancy and correlation analyses revealed that soil pH and organic carbon content were the most important factors driving these changes.Our findings provided a dynamic overview of the fungal community and presented a clear scope for screening beneficial fungi and pathogens of sweet potato.

Bacterial community shifts in different functional zones of a reservoir with ecological purification facilities

Ecological purification in a reservoir is an important strategy to control the level of nutrients in water.The bacterial community of such a reservoir is the main agent for pollutant degradation,which has not been fully documented.Taking the Jinze Reservoir,a freshwater source for Shanghai,China as the case,its spatial distributions of water and sediment bacteria were determined using 16S rRNA gene-based Illumina MiSeq sequencing,and the environmental parameters were analyzed.The reservoir takes natural river water and functions as an ecological purification system,consisting of three functional zones,i.e.,pretreatment zone,ecological purification zone,and ecological sustaining zone.Results show that the concentrations of both total nitrogen(TN)and total phosphorus(TP)decreased considerably after the ecological treatment,and the concentration of dissolved oxygen(DO)in the ecological purification zone was boosted from that before pretreatment.In addition,patterns of bacterial communities in both water and sediment were similar and consisted of mainly Proteobacteria,Actinobacteria,and Bacteroidetes.However,difference in water bacterial composition was distinct in each functional zone,whereas the bacterial communities in sediment changed only slightly among sediment samples.Network analysis revealed nonrandom co-occurrence patterns of bacterial community composition in water and sediment,and Pseudomonas,unclassified Comamonadaceae,Variovorax,and Dechloromonas were the key taxa in the co-occurrence network.The bacterial taxa from the same module of the network had strong ecological connections,participated in C-cycles,and shared common trophic properties.PICRUSt analysis showed that bacteria were involved potentially in various essential processes;and the abundance of predicted xenobiotic biodegradation genes showed a decreasing trend in water samples from the inlet to the outlet of the reservoir.These results improve our current knowledge of the spatial distribution of bacteria in water and sediment in ecological purification reservoirs.

Variations in microbial community during nitrogen removal by in situ oxygen-enhanced indigenous nitrogen-removal bacteria

In this study, the enclosure system exhibited perfect nitrogen removal performance with in situ oxygen-enhanced indigenous aerobic denitrifying bacteria in an enclosure experiment. We explored changes in the microbial community during the nitrogen removal process using the MiSeq high-throughput sequencing technology. The results revealed a total of 7974 and 33653 operational taxonomic units(OTUs) for water and sediment systems, respectively, with 97% similarity. The OTUs were found to be affiliated with eight main phyla(Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Firmicutes, and Actinobacteria). The diversity of the enhanced system was found to be higher than that of the control system. Principal component analysis(PCA) revealed that significant spatial and temporal differences were exhibited in the microbial community during nitrogen removal in the enclosure experiment. Redundancy analysis(RDA)indicated that physical parameters(temperature, dissolved oxygen, and pH), nitrogen(total nitrogen and nitrate), functional genes(nirK and nirS), and dissolved organic carbon(DOC) were the most important factors affecting bacterial community function and composition. Lastly, the results suggested that the variation in the microbial community could be analyzed through the MiSeq high-throughput sequencing technology,which may provide technical support for future field tests.

Soil Bacterial Communities Under Different Long-Term Fertilization Regimes in Three Locations Across the Black Soil Region of Northeast China

Although soil bacteria play critical roles in agro-ecosystems, the knowledge of their response to long-term fertilization across the black soil region of Northeast China is limited. In this study, we sequenced 16 S rRNA genes to assess the effects of four long-term fertilization regimes—non-fertilization(NoF), chemical fertilizer(CF), manure(M), and chemical fertilizer plus manure(CFM)—on soil properties and bacterial communities in three locations, the northern, middle, and southern parts, across the black soil region. Results showed that the influence of fertilization regimes on soil properties varied significantly among the three locations. Manure fertilization significantly increased microbial biomass carbon and relative abundance of copiotrophic bacteria. Principal component analysis(PCA)showed that the total bacterial communities were separated into three groups according to the sampling location despite long-term fertilization, and that soil pH was the most important factor in shifting bacterial communities. In addition, similar fertilization regimes resulted in different influences on bacterial community composition, and the most influential soil properties varied among the three locations. Our results highlighted that geographical separation was a more dominant factor affecting bacterial communities than fertilization, and that long-term similar fertilization regimes did not induce consistent changes in bacterial community composition in the black soil region.

Illumina-Based Analysis of Bulk and Rhizosphere Soil Bacterial Communities in Paddy Fields Under Mixed Heavy Metal Contamination

There is an increasing concern about rice （Oryza sativa L.） soil microbiomes under the influence of mixed heavy metal contamina- tion. We used the high-throughput Illumina MiSeq sequencing approach to explore the bacterial diversity and community composition of soils in four paddy fields, exhibiting four degrees of mixed heavy metal （Cd, Pb and Zn） pollution, and examined the effects of these metals on the bacterial communities. Our results showed that up to 2 104 to 4 359 bacterial operational taxonomic units （OTUs） were found in the bulk and rhizosphere soils of the paddy fields, with the dominant bacterial phyla （greater than 1% of the overall community） including Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, Chlorofiexi, Bacteroidetes and Nitrospirem. A number of rare and candidate bacterial groups were also detected, and Saprospirales, HOC36, SC-I-84 and Anaerospora were rarely detected in rice paddy soils. Venn diagram analysis showed that 174 bacterial OTUs were shared among the bulk soils with four pollution degrees. Rice rhizosphere soils displayed higher bacterial diversity indices （ACE and Chao 1） and more unique OTUs than bulk soils. Total Cd and Zn in the soils were significantly negatively correlated with ACE and Chao 1, respectively, and the Mantel test suggested that total Pb, total Zn, pH, total nitrogen and total phosphorus significantly affected the community structure. Overall, these results provided baseline data for the bacterial communities in bulk and rhizosphere soils of paddy fields contaminated with mixed heavy metals.

Long-term agricultural contamination shaped diversity response of sediment microbiome

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 16 S 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.

Variations regularity of microorganisms and corrosion of cast iron in water distribution system

Corrosion, one of the most common problems of metal pipe for water supply, generally leads to poor water quality, bacteria proliferation, water capacity decrease and other problems. As microorganisms affect corrosion by changing the characteristics of metal surface, the mechanism of microbial corrosion still remains unclear. The corrosion behavior of ductile cast iron is implemented in the dynamic flow and static conditions, in which variations of water quality and microbial community are analyzed in details. The results show that if the corrosion rate of ductile cast iron decreases, the corrosion of cast iron will result in a lower DO and a higher total iron in bulk water. The number of microorganisms is not a decisive factor of corrosion, even though the counts of bacteria had a close relationship with DO. On the basis of the detection of the 10 kinds of nitratereducing bacteria by Miseq sequencing, NRB of the biofilm biomass accounts for 18.3% on the 30 th day and 20.5% on the 55 th day. Even though aerobic NRBs go into the biofilm later than the facultative anaerobic NRBs, the growth of the anaerobic NRBs is not affected.

Earthworm rather than biochar and sodium silicate addition increased bacterial diversity in mining areas subjected to chemical fertilization

The addition of biochar,sodium silicate,or earthworm is a feasible practice to repair soils disturbed by mining activities,and the reclamation is largely based on the alteration of the diversity and structure of soil bacteria.The objectives of this study were to assess the relative importance of these supplements on soil bacterial community diversity and structure in reclaimed mine areas.A field experiment with soybean was carried out in mining areas to assess the efficiency of nitrogen,phospho-rus and potassium(NPK)fertilizers plus those supplements on soil bacterial community structure and diversity by the 16S rRNA sequencing method.Soil chemical properties were analyzed to their effects on the bacterial community structure.The results showed that the application of nitrogen,phosphorus and potassium(NPK)fertilizers significantly increased bacterial diversity,and a further increase was observed in NPK plus biochar,sodium silicate or earthworm addition.Furthermore,a higher number of genera were found in the NPK plus biochar and NPK plus earthworm treatments than that in the control,NPK and NPK plus sodium silicate treatments.The bacterial community was significantly associated with nutrients,such as carbon(C)and nitrogen(N).Moreover,soil organic carbon(SOC)and pH were the most dominant factors in shaping the soil bacterial community structure and diversity.Our data indicate that the addition of earthworms to soil rather than biochar and sodium silicate was the best strategy to mitigate the detrimental effects of mining activities on soil bacterial diversity.