Dominant Operational Taxonomic Units Research Articles

Investigation of soil microbiota reveals variable dominant species at different land areas in China

Soil microbiota is associated with plant growth and nutrition. Investigation of plant–soil interaction is essential for revealing the changes of microbial dynamics in the soil. Vegetation types and human activities, such as agriculture, had severely affected soil microbial structure and function. In this study, 16S rRNA were analysed to identify microbial structures in the soil. The total organic carbon (TOC) and total nitrogen (TN) in these soil samples were also analysed. TOC and TN in these soil samples were different, which might be due to different vegetation types. The main phyla in these soil samples were Actinobacteria, Proteobacteria and Acidobacteria. Furthermore, the genera in these soil groups were highly diverse, and most of the bacteria could not be assigned to any known genus. This indicated the presence of novel bacterial genera in these soil samples. A fraction of the dominant operational taxonomic units in the soil microbiota was identified, several of which played functional roles in soil nutrition. The linkage between the soil microbiota, especially the dominant species, and soil nutrients was analysed in this study. The culturomics and other omics technologies would help to isolate some novel microorganisms, which might lead to the recovery of functional microbial agents for plant growth.

Dominance of arbuscular mycorrhizal fungi is key for Mongolian steppe management under livestock grazing, as indicated by ecosystem multifunctionality

Livestock grazing of drylands supports millions of livelihoods worldwide; however, overgrazing causes severe biodiversity loss and degrades ecosystem functions. Understanding the effects of grazing intensity, aridity, and soil microbes is required for sustainable management. Here, we focused on arbuscular mycorrhizal (AM) fungi in soils and roots and examined their relationship with ecosystem multifunctionality under livestock grazing of Mongolian grasslands with different aridity levels. Above- and below-ground plant biomass were used to measure ecosystem-service multifunctionality, excluding annual plants that are unfavorable for ecosystem function and rangeland management. In both mountain forest steppe (mean annual precipitation = 207.7 mm) and steppe–desert steppe transition zone (mean annual precipitation = 128.4 mm), ecosystem multifunctionality was decreased by livestock grazing, as indicated by palatable plant shoot biomass. In line with the multifunctionality, the dominant plant species, Stipa krylovii, and AM plant biomass were decreased by livestock grazing. The Berger–Parker dominance index of soil AM fungi and Simpson’s diversity had a positive and negative relationship with multifunctionality, respectively, indicating that dominant AM fungi rather than AM fungal diversity in soil are key for maintaining multifunctionality. Root and soil AM fungal communities were significantly different with dominance of Rhizophagus operational taxonomic units (OTUs) in roots and Claroideoglomus OTUs in soil. However, the similarity between soil and root AM fungal communities increased with livestock grazing. Correlation analysis between palatable plant biomass and relative abundance of dominant AM fungal OTUs identified indicator virtual taxa that decreased (VTX00325 in roots, and VTX00165, VTX00214, and VTX00222 in soil) or increased (VTX00100, VTX00130, and VTX00295 in soil) with grazing intensity. The OTUs that were increased by grazing may be r-selected, grazing-tolerant AM fungi that accept a low C supply and supply few nutrients to plants. Our results suggest that grassland management focusing on ecosystem-service multifunctionality via control of AM plants, including S. krylovii and their co-dominant dominant AM fungi, in ungrazed grasslands are key for sustainable rangeland management in Mongolia.

Bacterial Communities in Coral Offspring Vary Between in situ and ex situ Spawning Environments

Examining the bacterial communities of offspring is key to understanding the establishment of coral-bacteria associations. Although high sensitivity to the environment is expected, previous studies have only examined bacterial communities of coral offspring in ex situ (laboratory) environments, not in in situ (field) environments. Here, we examined and compared the effect of ex situ and in situ environments on bacterial communities of newly released offspring (eggs and larvae) and their maternal colonies in two phylogenetically distant coral species with different reproductive modes: Dipsastraea speciosa (Scleractinia; spawner) and Heliopora coerulea (Octocorallia; brooder). Our results demonstrated that the spawning environments do not affect the bacterial composition in maternal colonies, but influence that of the offspring (eggs of D. speciosa and larvae of H. coerulea). Dominant bacterial operational taxonomic units (OTUs) varied between in situ and ex situ environments in the eggs of D. speciosa. The composition of bacterial communities among larvae of H. coerulea samples was more diverse in in situ environments than in ex situ environments. This study provides the first information on in situ bacterial communities in coral eggs and larvae and highlights their sensitivities to the local environment. Future studies must take into consideration the influence of ex situ environments on bacterial communities in coral offspring.

Determining the Microbial Source of Methane Production in Anaerobic Digestion Systems Through High-Throughput Sequencing Technology

Anaerobic digestion is widely used to simultaneously generate biogas while treating different organic wastes. It is difficult to determine the source of CH4 from the complex microbial community structure using traditional microbiological pure culture techniques. Therefore, this study aimed to elucidate the microbial source of CH4 in low-temperature anaerobic digestion systems using the recently developed high-throughput sequencing technology. Herein, anaerobic digestion microbes were domesticated at 15°C and then inoculated into pig manure-containing raw materials in a batch anaerobic digester to form a low-temperature anaerobic digestion system with fermentation controlled at 15°C. Several analytical approaches including abiotic factor analysis and biotic factor analysis (high-throughput sequencing) were applied to investigate the abiotic factors, bacterial communities, and archaeal communities in the low-temperature anaerobic digestion system. The results showed that: 1) The anaerobic digestion lasted for 120 days, with 68.65 L total gas production and 31.19 L CH4 production. 2) The relative abundances of the primary and secondary dominant bacterial operational taxonomic units ranged from 8.02 to 22.84% and 5.62–17.09%, respectively, with 99% similarities to Clostridium cellulovorans (a typical cellulose- and hemicellulose-degrading bacterium) and Terrisporobacter petrolearius (a representative fermentation bacterium), respectively. Moreover, the relative abundance of the primary dominant methanogenic archaeal operational taxonomic unit ranged from 1.03 to 16.85%, with 98% similarity to Methanobacterium beijingense, which is a typical hydrogenotropic methanogen. Based on the low-temperature CH4-producing metabolic pathways of bacterial and methanogenic operational taxonomic units, Methanobacterium beijingense was found to be the primary functional microbe for CH4 production in the 15°C anaerobic digestion system.

水产养殖不同物种对水体和沉积物中细菌群落的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 水产养殖不同物种对水体和沉积物中细菌群落的影响 DOI: 10.5846/stxb202103190734 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 水体污染控制与治理科技重大专项（2017ZX07301006）；江苏省渔业科技类项目：池塘工业化生态养殖系统净水区水质优化技术研究（D2017-2-2） Effects of different aquacultural species on planktonic and sedimental bacterial communities Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为探究水产养殖中养殖不同物种对水体和沉积物中细菌群落的影响，以养殖克氏原螯虾（Procambarus clarkii，PC）和中华鳖（Pelodiscus sinensis，PS）的水体和沉积物样品为研究对象，利用基于16S rRNA基因的高通量测序技术，对细菌群落多样性和群落组成进行分析，并结合环境因子，探究水产养殖对细菌群落的影响。结果显示，水体和沉积物中细菌群落的α多样性均呈现PS>PC的显著差异（P<0.05）。非度量多维尺度分析的结果显示，PC和PS区的水体和沉积物细菌群落结构均呈现明显差异。冗余分析（RDA）的结果表明，水体氨氮（NH4+-N）和硝酸盐氮（NO3--N）是影响水体细菌群落结构的最主要环境因子，沉积物总氮（TN）、总磷（TP）和有机碳（OC）均对沉积物细菌群落结构有显著影响（P<0.05）。PC和PS区中的细菌隶属于34门、114纲、258目、504科和955属，水体中共筛选出了11个优势菌门（相对丰度>0.5%），沉积物中筛选出了13个。2个养殖区域的水体样品中共筛选出了15个优势（相对丰度>1%）操作分类单元（Operational Taxonomic Unit，OTU），其中有9个具有脱氮除磷或去除有机质的作用，它们分别属于丛毛单胞菌科（Comamonadaceae）、腐螺旋菌科（Saprospiraceae）、嗜甲基菌属（Methylophilus）、放线菌目（Actinomycetales）和沉积杆菌属（Sediminibacterium）。整体上，这9个优势OTUs在PC区中的相对丰度更高，并且与氨氮（NH4+-N）和硝酸盐氮（NO3--N）的相关性较强。同时，在沉积物样品中筛选出了7个优势OTUs，其中有3个主要参与氮循环，它们分别属于Dechloromonas属、Prolixibacteraceae科和厌氧绳菌科（Anaerolineaceae）。此外，在水体样品中发现了3个优势OTUs为致病菌，分别属于黄杆菌属（Flavobacterium）和多核杆菌属（Polynucleobacter）。综合以上分析，养殖不同物种会对水体和沉积物中细菌群落多样性和结构产生不同影响。 Abstract:In order to investigate the effects of different aquacultural species (Procambarus clarkii, PC and Pelodiscus sinensis, PS) on planktonic and benthic bacterial communities, water and sediment samples were collected. The α-diversity, compositions and abundance of the planktonic and benthic bacterial community were analyzed using high-throughput sequencing targeted the 16S rRNA genes. The influence of environmental factors on bacterial communities was also examined. The results showed that, for both water and sediment samples, the α-diversity of bacterial community within PS zone was significantly higher than that of the PC zone (P<0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that the bacterial community composition of the water and sediment samples were significantly different between the two zones. Redundancy analysis (RDA) showed that ammonia nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) were the main factors that affected the bacterial community composition in the water samples. Total nitrogen (TN), total phosphorus (TP), and organic carbon (OC) had significant effects (P<0.05) on the bacterial community composition in the sediment samples. 34 phyla, 114 classes, 258 orders, 504 families, and 955 genera of bacterial communities were obtained totally from the water and sediment samples in the two zones. High-throughput sequencing analysis indicated that there were eleven and thirteen dominant phyla (relative abundance>0.5%) of bacterial communities within water and sediment samples, respectively. We found fifteen and seven dominant (relative abundance>1%) operational taxonomic units (OTUs) in water samples and sediment samples, respectively. In water samples, there were nine dominant OTUs could remove nutrients, and they were belonged to Comamonadaceae, Saprospiraceae, Methylophilus, Actinomycetales and Sediminibacterium, respectively. The relative abundance of these nine dominant OTUs within PC zone was higher than that of the PS zone in general. And the relative abundance of the eight of them was significantly positively correlated (P<0.01) with NH4+-N and NO3--N. In sediment samples, there were three dominant OTUs played important roles in the nitrogen cycle, and they were belonged to Dechloromonas, Prolixibacteraceae and Anaerolineaceae, respectively. Furthermore, three dominant OTUs in water samples were detected as pathogens, which belonged to Flavobacterium and Polynucleobacter, respectively. Pearson correlation analysis demonstrated that the relative abundance of the three dominant OTUs which were detected as pathogens were significantly positively correlated (P<0.01) with NH4+-N and NO3--N. Based on the above results, different aquacultural species had different effects on bacterial community diversity and composition of water and sediment. 参考文献 相似文献 引证文献

RNA Virosphere in a Marine Zooplankton Community in the Subtropical Western North Pacific.

Zooplankton and viruses play a key role in marine ecosystems; however, their interactions have not been examined in detail. In the present study, the diversity of viruses associated with zooplankton collected using a plankton net (mesh size: 100‍ ‍μm) in the subtropical western North Pacific was investigated by fragmented and primer ligated dsRNA sequencing. We obtained 21 and 168 operational taxonomic units (OTUs) of ssRNA and dsRNA viruses, respectively, containing RNA-dependent RNA polymerase (RdRp). These OTUs presented average amino acid similarities of 43.5 and 44.0% to the RdRp genes of known viruses in ssRNA viruses and dsRNA viruses, respectively. Dominant OTUs mainly belonged to narna-like and picorna-like ssRNA viruses and chryso-like, partiti-like, picobirna-like, reo-like, and toti-like dsRNA viruses. Phylogenetic ana-lyses of the RdRp gene revealed that OTUs were phylogenetically diverse and clustered into distinct clades from known viral groups. The community structure of the same zooplankton sample was investigated using small subunit (SSU) rRNA sequences assembled from the metatranscriptome of single-stranded RNA. More than 90% of the sequence reads were derived from metazoan zooplankton; copepods comprised approximately 70% of the sequence reads. Although this ana-lysis provided no direct evidence of the host species of RNA viruses, these dominant zooplankton are expected to be associated with the RNA viruses detected in the present study. The present results indicate that zooplankton function as a reservoir of diverse RNA viruses and suggest that investigations of zooplankton viruses will provide a more detailed understanding of the role of viruses in marine ecosystems.

Novel members of bacterial community during a short-term chilled storage of common carp (Cyprinus carpio)

This work aimed to identify the key members of the bacterial community growing on common carp (Cyprinus carpio) fillets during chilled storage with next-generation sequencing (NGS) and cultivation-dependent methods. Carp fillets were stored for 96 h at 2 °C and 6 °C with and without a vacuum package, and an additional frozen-thawed storage experiment was set for 120 days. Community profiles of the initial and stored fish samples were determined by amplicon sequencing. Conventional microbial methods were used parallelly for the enumeration and cultivation of the dominant members of the microbial community. Cultivated bacteria were identified with 16S rRNA sequencing and the MALDI-TOF MS method. Based on our results, the vacuum package greatly affected the diversity and composition of the forming microbial community, while temperature influenced the cell counts and consequently the microbiological criteria for shelf-life of the examined raw fish product. Next-generation sequencing revealed novel members of the chilled flesh microbiota such as Vagococcus vulneris or Rouxiella chamberiensis in the vacuum-packed samples. With traditional cultivation, 161 bacterial strains were isolated and identified at the species level, but the identified bacteria overlapped with only 45% of the dominant operational taxonomic units (OTUs) revealed by NGS. Next-generation sequencing is a promising and highly reliable tool recommended to reach a higher resolution of the forming microbial community of stored fish products. Knowledge of the initial microbial community of the flesh enables further optimization and development of processing and storage technology.

Archaeal Communities of Frozen Quaternary Sediments of Marine Origin on the Coast of Western Spitsbergen

The archaeal composition of permafrost samples taken during the drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. This study is based on an analysis of the V4 region of the 16S rRNA gene, carried out using next-generation sequencing. The general phyla of the Archaea domain are Euryarchaeota, Bathyarchaeota, Thaumarchaeota, and Asgardarchaea. As a result of a phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic and methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea, are found. The methanogenic archaea of Euryarchaeota phylum, Methanobacteria class, are found in permafrost with controversial genesis, while the methane-oxidizing archaea of Methanomicrobia class Methanosarcinales order are found in the marine permafrost at cape Finneset: the ANME-2a, -2b group in layers of 8.6 and 11.7 m and the ANME-2d group (Candidatus Methanoperedens) in a layer of 6.5 m. Ammonium-oxidizing archaea of phylum Thaumarchaeota is present in all types of permafrost, while the order of Nitrososphaerales is found in permafrost with controversial genesis and the order Nitrosopumilales is in permafrost with marine and controversial genesis. Representatives of phylum Bathyarchaeota are found stratigraphically in the most ancient samples under study. Asgardarchaeota superfylum is excluded in the layers of permafrost with marine genesis and is represented by the phyla Lokiarchaeota, Thorarchaeota, and an unclassified group belonging to this superphylum. The presence of methane, ethylene, and ethane in the permafrost of the first sea terrace of Cape Finnemet at a depth of 11.7 m, as well as the composition of the archaeal community, give us reason to assume that, before freezing, microbiological processes of anaerobic methane oxidation took place in it, probably received from Tertiary rocks. The results of both this and previous works present the Spitsberen permafrost as a rich archive of genetic information of little-studied prokaryotic groups.

Sex Differences in Fecal Microbiota Correlation With Physiological and Biochemical Indices Associated With End-Stage Renal Disease Caused by Immunoglobulin a Nephropathy or Diabetes.

This study investigated the sex-specific differences in the correlation between intestinal microbiota and end-stage renal disease. Here, we compared the differences in the gut microbiota of male and female healthy controls (HC) and patients with end-stage renal disease (ESRD) caused by immunoglobulin A (IgA) nephropathy (ESRD-IgAN) or type-2 diabetes mellitus (ESRD-T2DM) using high-throughput sequencing of the 16S rRNA gene. We also analyzed the correlation between gut microbiota and clinical immune indicators. We assigned 8, 10, 5, 7, 11, and 20 volunteers to female HC, ESRD-IgAN, and ESRD-T2DM, and male HC, ESRD-IgAN, and ESRD-T2DM, respectively. The results showed sex-specific differences in both physiological and biochemical indices and intestinal microbiota composition, as well as the correlation between them. The correlations between physiological and biochemical indices in men were significantly lower than those in women, especially for indices related to immunity, blood glucose, and cardiac color sonography. Urine output, lymphocyte ratio, serum albumin, blood calcium, dialysis status, serum urea nitrogen, urine protein, and diabetes significantly correlated with male fecal microbiota composition, whereas only creatinine and 2-h post-prandial blood glucose significantly correlated with female fecal microbiota composition. The top 50 dominant operational taxonomic units showed a stronger correlation with physiological and biochemical indices in samples obtained from females than from males. These differences highlight sex-specific differences in the effectiveness of ESRD prevention and treatments via regulating intestinal microbiota.

Hexavalent Chromium Removal and Prokaryotic Community Analysis in Glass Column Reactor Packed with Aspen Wood as Solid Organic Substrate.

Microbial hexavalent chromium (Cr(VI)) reduction is a promising method for Cr(VI)-laden wastewater treatment. However, the soluble organic substrate required for heterotrophic microbial Cr(VI) reduction necessitates constant supervision, and an excessive supply of soluble organic substrate can result in deterioration of the quality of the effluent. In this study, we evaluated aspen wood, a low-cost lignocellulose biomass, as a solid organic substrate for heterotrophic Cr(VI) reduction. A laboratory-scale aspen wood-packed glass column reactor inoculated with activated sludge was operated for 148days for evaluation. Following reactor operation, an effective average dissolved Cr(VI) removal rate of 0.75mg L-1h-1 was confirmed under an average dissolved Cr(VI) loading rate of 0.90mg L-1h-1. Subsequently, 16S ribosomal ribonucleic acid gene amplicon sequencing analysis revealed that the dominant prokaryotic operational taxonomic units detected in the reactor were associated with prokaryotic lineages with the capacity for lignocellulose biodegradation, Cr compound resistance, and Cr(VI) reduction. Proteobacteria and Chloroflexi were two major prokaryotic phyla in the reactor. Our data indicate that aspen wood is an effective solid organic substrate for the development of simplified, effective, and low-cost microbial Cr(VI)-removing reactors.

Detection of Pathogenic and Beneficial Microbes for Roselle Wilt Disease.

Wilt disease of roselle (Hibiscus sabdariffa L.) is common in Taiwan; however, the causative agent remains unknown. The stems of wilted roselle are browned, slightly constricted, and covered by white aerial hyphae, suggesting that potential pathogens may originate from soil. To identify the potential pathogens, we conducted a rhizosphere microbiota survey in phenotypically healthy and diseased plants through fungal internal transcribed spacer (ITS) and bacterial 16S rRNA amplicon sequencing for uncovering the microbial compositions in the roselle rhizosphere. The fungal family Nectriaceae exhibited significantly higher abundance in diseased rhizospheres than in healthy rhizospheres, and this bacterial community was more specific to geography (i.e., plot-dependent) than to rhizosphere disease status. However, a few bacterial groups such as Bacilli were associated with the healthy rhizosphere. Fusarium species were the most dominant species of Nectriaceae in the survey and became the main target for potential pathogen isolation. We successfully isolated 119 strains from diseased plants in roselle fields. Koch’s postulates were used to evaluate the pathogenicity of these strains; our results indicated that Fusarium solani K1 (FsK1) can cause wilting and a rotted pith in roselles, which was consistent with observations in the fields. This is the first demonstration that F. solani can cause roselle wilt in Taiwan. Furthermore, these newly isolated strains are the most dominant operational taxonomic units detected in ITS amplicon sequencing in diseased rhizospheres, which serves as further evidence that F. solani is the main pathogen causing the roselle wilt disease. Administration of Bacillus velezensis SOI-3374, a strain isolated from a healthy roselle rhizosphere, caused considerable anti-FsK1 activity, and it can serve as a potential biocontrol agent against roselle wilt disease.

A high abundance of Firmicutes in the intestine of chinese mitten crabs (Eriocheir sinensis) cultured in an alkaline region

The Chinese mitten crab (Eriocheir sinensis) is a popular aquaculture product in East Asia, especially in China. In the last decade, rice–crab co-culture has rapidly expanded in China. Under this model, crabs are raised in rice fields instead of in traditional aquaculture ponds. In this study, we cultured two varieties of Chinese mitten crabs (Changjiang and Liaohe) in an alkaline region in northwest China and used Illumina MiSeq sequencing to compare the intestinal bacterial alpha diversity and community structure between traditional and co-culture aquaculture models, between two crab varieties, and between female and male crabs. Significant variations in intestinal bacterial communities were found between crab varieties and between female and male crabs but not between aquaculture models. These results show that rice–crab co-culture operations did not obviously impact the crab intestinal bacterial community compared with traditional pond aquaculture. Firmicutes was the most abundant bacterial phylum in the crab intestines (78%, relative abundance). Three dominant operational taxonomic units (OTUs) represented 73.2% of Firmicutes sequences and 56.8% of all sequences. A dominant OTU assigned as Firmicutes that was negatively correlated with crab body length, width, and weight was found in the source water for the experimental area. The results of this study suggest that the aquaculture of Chinese mitten crabs in alkaline regions requires more study to improve cultivation techniques.

Revealing the dissimilar structure of microbial communities in different WWTPs that treat fish-canning wastewater with different NaCl content

Studies that characterize the microbial communities in wastewater treatment plants (WWTPs) are numerous, yet similar studies in industrial WWTPs treating fish-canning effluents are limited. The microbial communities in samples of 4 fish-canning WWTPs that operated under different NaCl concentrations were investigated by qPCR and partial 16S rRNA gene Illumina sequencing. The absolute abundances of key microbial populations (Total Bacteria, Archaea and Fungi, ammonium oxidizing bacteria (AOB), Mycolata, Candidatus Microthrix, Ca. Accumulibacter and Ca. Competibacter) presented statistical differences among the WWTPs. The NaCl concentration negatively affected the absolute abundance of Bacteria and Fungi, filamentous, and phosphate (PAO) and glycogen (GAO) accumulating bacteria, while AOB and Ca. Microthrix populations were statistically higher in the WWTP with higher NaCl contents. On the other hand, the main bacterial operational taxonomic units (OTUs) were classified as members of Kouleothrix (Chloroflexia, Chloroflexi) and Tetrasphaera (Actinomycetia, Actinobacteria), family Beijerinckiaceae (Alphaproteobacteria, Proteobacteria), order Betaproteobacteriales (Gammaproteobacteria, Proteobacteria), Sphingobacteriales (Sphingobacteriia, Bacteroidetes) and Frankiales (Actinobacteria, Actinobacteria), class Anaerolineae (Chloroflexi), phylum Chloroflexi and Bacteria_unclassified. The structure of the bacterial community was highly dissimilar among the 4 WWTPs, as the identities of the dominant OTUs differed significantly among them. Therefore, the individual characteristics of the different WWTPs, mainly NaCl concentration, were responsible for the narrow assemblage of the bacterial communities. Different OTUs belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Proteobacteria were revealed as salt-tolerant. Taking into account these results, NaCl content was an important driver of the abundance of microbial populations and the bacterial community structure in the analysed industrial facilities.

Characterization of bacterial DNA identified in abscessed and non-abscessed bovine hepatic tissue at the time of harvest.

Bacteriological characterization of bovine liver abscesses has been accomplished by cultural methods but DNA methods are still needed, as many bacteria are not conducive to laboratory culture. In addition to this gap in research, there have been no studies which identify the bacterial presence within healthy, non-abscessed liver tissue. The objective of this study was to compare the bacteriome of both abscessed and non-abscessed bovine livers in an observational case–control study design. Fifty-six livers, obtained from Holstein steers, were scored according to a modified Elanco liver abscess score description where A− was partitioned into active abscesses or scarred where only scars were present. Parenchyma tissue was collected from non-abscessed livers (n = 22) and scarred livers (n = 7), and purulent material was collected from abscessed livers (n = 24), and DNA was extracted for 16s rRNA gene sequence-based bacterial analysis. Across liver samples, 21 total phyla were identified with a mean of 14. Predominant phyla, accounting for >98% of reads, were Fusobacteria (51.7%), Bacteroidetes (26.9%), Proteobacteria (8.03%), Firmicutes (5.39%), Cyanobacteria (3.85%), and Actinobacteria (2.21%). Proteobacteria, Cyanobacteria, and Firmicutes were greater in non-abscessed and scarred livers, whereas Fusobacteria and Bacteroidetes prevailed in abscessed livers. Non-abscessed livers shared 3,059 operational taxonomic units (OTU) with abscessed livers (total OTU of all livers = 4,167), but non-abscessed livers had greater richness and evenness, whereas abscessed livers had greater dominance (P ≤ 0.0014). Liver score affected the relative abundance of OTU (R = 0.463; P = 0.001) but abscessed livers shared ≥ 40% similarity and were not different from each other (P ≥ 0.370). Of the predominant OTU (top 10 as a % of reads), three OTU (Fusobacteria necrophorum, Bacteroides spp., and Trueperella pyogenes) were shared across both abscessed and non-abscessed livers. Fusobacterium necrophorum was the dominant OTU regardless of liver score, and the single most abundant OTU, even among non-abscessed livers. We describe bacterial DNA detected in non-abscessed bovine liver tissue for the first time, which indicates possible presence of viable bacteria with pathogenic potential in apparently healthy liver tissue.

Molecular diversity of arbuscular mycorrhizal fungi associated with two alpine plant species in the Tibetan Plateau

Alpine ecosystem in the Tibetan Plateau has a special ecological environment, which may harbor a high richness of arbuscular mycorrhizal fungi (AMF) communities. To explore the molecular diversity of AMF community associated with plants in alpine grasslands, root and rhizosphere soil of two dominant plant species, Kobresia sp. and Leontopodium pusillum in Qinghai province, were studied by molecular biotechnology (clone library and sequencing) at five sites for each plant species. A total of 30 operational taxonomic units (OTUs) were identified, including seven families of Glomeromycota. Glomeraceae and Glo1 and Glo2 were most abundant at family and OUT level in roots respectively, while both Glomeraceae and Diversisporaceae were frequently present and Glo1 and Div1 were the most dominant OTUs in the soil. The AMF community was different in the roots and soil. Nineteen OTUs were identified in the roots of Kobresia sp., and 21 OTUs were identified in the rhizosphere soil. As to L. pusillum, fourteen OTUs were identified in roots and 17 OTUs in the soil. Specifically, three OTUs were only found in L. pusillum, and eight OTUs were only found in Kobresia sp. The root biomass and soil C/N ratio were the main factors affecting the AMF community in roots, whereas in soil, the important factors were root carbon content and shoot nitrogen content. These results showed a high diversity of AMF associated with the typical alpine plants, and distinct AMF community exist in roots and soil. Our results confirmed the importance of plant and soil factors in driving AMF assemblages in the fragile ecosystem of Tibetan Plateau.

Evaluating the Health Risks of Pneumonia from Airborne Bacterial Communities Using 16S rDNA Sequences of Pneumonia-related Pathogens

ObjectiveAirborne microbial communities include a significant number of uncultured and poorly characterized bacteria. No effective method currently exists to evaluate the health risks of such complex bacterial populations, particularly for pneumonia. MethodsWe developed a method to evaluate risks from airborne microorganisms, guided by the principle that closer evolutionary relationships reflect similar biological characteristics, and thus used 16S rDNA sequences of 10 common pneumonia-related bacterial pathogens. We calculated a risk of breath-related (Rbr) index of airborne bacterial communities and verified effectiveness with artificial flora and a clinical project. ResultsWe suggested applying Rbr80 to evaluate the health risks of airborne bacterial communities that comprise 80% of dominant operational taxonomic units (OTUs). The feasibility of Rbr80 was confirmed by artificial flora and by pneumonia data from a hospital. A high Rbr80 value indicated a high risk of pneumonia from airborne bacterial communities. ConclusionRbr80 is an effective index to evaluate the pneumonia-associated risk from airborne bacteria. Values of Rbr80 greater than 15.40 are considered high risk.

Seasonal Distribution of Cyanobacteria in Three Urban Eutrophic Lakes Results from an Epidemic-like Response to Environmental Conditions.

Cyanobacterial communities of three co-located eutrophic sandpit lakes were surveyed during 2016 and 2017 over season and depth using high-throughput DNA sequencing of the 16S rRNA gene. All three lakes were stratified except during April 2017 when the lakes were recovering from a strong mixing event. 16S rRNA gene V4 sequences were parsed into operational taxonomic units (OTUs) at 99% sequence identity. After rarefaction of 139 samples to 25,000 sequences per sample, a combined total of 921,529 partial 16S rRNA gene sequences were identified as cyanobacteria. They were binned into 19,588 unique cyanobacterial OTUs. Of these OTUs, 11,303 were Cyanobium. Filamentous Planktothrix contributed 1537 and colonial Microcystis contributed 265. The remaining 6482 OTUs were considered unclassified. For Planktothrix and Microcystis one OTU accounted for greater than 95% of the total sequences for each genus. However, in both cases the non-dominant OTUs clustered with the dominant OTUs by date, lake, and depth. All Planktothrix OTUs and a single Cyanobium OTU were detected below the oxycline. All other Cyanobium and Microcystis OTUs were detected above the oxycline. The distribution of Cyanobium OTUs between lakes and seasons can be explained by an epidemic-like response where individual OTUs clonally rise from a diverse hypolimnion population when conditions are appropriate. The importance of using 99% identity over the more commonly used 97% is discussed with respect to cyanobacterial community structure. The approach described here can provide another valuable tool for assessing cyanobacterial populations and provide greater insight into the controls of cyanobacterial blooms.

Warming rather than elevated CO2 shifts the rhizobacterial community composition in four maize‐growing soils

AbstractClimate change may fundamentally affect the microorganisms in the rhizosphere that drive soil C and nutrient cycles. This study aimed to clarify the response of rhizobacterial community to warming and elevated CO2 (eCO2) in typical maize (Zea mays L.)‐growing soils. Under climate change, the shift of rhizobacterial community composition was assumed to be different among soils, which would be associated with the C sequestration and stability in soils. Using open‐top chambers to mimic climate warming and eCO2, we examined the taxonomic composition of bacterial communities in the rhizosphere of maize grown in four farming soils (Acrisol, Fluvisol, Kastanozem, and Phaeozem). Warming decreased the richness of the rhizobacterial community by 3.8% across the soils, but eCO2 did not significantly alter community richness. The shift in bacterial community composition was greater under warming than under eCO2, and the shift was different among soils. The abundance of Streptomyces and Gaiella significantly increased in Phaeozem and Acrisol in response to warming but not in Fluvisol or Kastanozem. Sphingomonas was suppressed in Phaeozem under warming, whereas Sphingomonas, Shinella, and Rhodospirillaceae_norank were enriched in the other three soils. Soil chemical characteristics including nitrate, Olsen P, available K, and soil organic C (SOC) were significantly associated with a number of dominant operational taxonomic units. These results indicate that the effect of warming on bacterial community composition in the rhizosphere of maize may be stronger than the effect of eCO2. Climate change led to various changes in the rhizobacterial community composition among soils that might be associated with the quality of SOC and nutrient status in different soils.

Significant Differences in Intestinal Microbial Communities in Aquatic Animals from an Aquaculture Area

While much attention has been given to the role of animal intestinal microbes, few studies have focused on microbial communities and associated functions in cultured aquatic animals. In this study, high–throughput sequencing was used to analyze intestinal microbial communities and functions in fish, shrimp, crab and razor clams. Alpha diversity analyses showed significant differences in intestinal microbial diversity amongst these aquatic animals, and that shrimp intestines harbored the highest diversity and species numbers. T–test analyses (p &lt; 0.05) showed significant differences in dominant microbial operational taxonomic units (OTUs) between all aquatic animals. Predominant intestinal bacteria included; Gammaproteobacteria, Fusobacteria, Mollicutes, Spirochaetia, Cyanobacteria, Bacteroidia and Bacilli. Similarly, anaerobic bacteria were highly diverse in animal intestines and included; Vibrio, Photobacterium, Cetobacterium, Propionigenium, Candidatus Hepatoplasma, Paraclostridium, and Lactobacillus. Principal co–ordinate analysis indicated that the distribution characteristics of intestinal microbes varied with animal species; in particular, we observed a high variability among shrimp intestinal samples. This variability indicated these genera had suitability for the different intestinal environment. Function prediction analysis indicated significant differences amongst different animals in the major functional groups, and that microbial functional profiles were strongly shaped by the intestinal environment. Thus, this study provides an important reference for future studies investigating crosstalk between aquatic animal hosts and their intestinal microbiota.

Soil microbiome after nine years of fly ash dump spontaneous revegetation

Fly ash dumps of thermal power stations have been increasing in area worldwide due to the growing demand for power. One of the cost-effective approaches for restoring such sites is spontaneous revegetation in those areas where adjacent indigenous ecosystems can supply seeds and living organisms. We assessed microbiome taxonomic diversity in a Technosol developed during nine years of spontaneous revegetation of the terminated fly ash pond of a thermal power station in Novosibirsk, Russia, in comparison with microbiome diversity in undisturbed Phaeozem under adjacent birch forest by using 16S (V3–V4) and ITS2 (ITS3–ITS4) amplicon sequencing with Illumina MiSeq. We identified 577 fungal and 5542 bacterial operational taxonomic units (OTUs); 95–99% of them were minor or rare species. The dominant OTUs were completely different in the studied soils. At the phylum level, the ultimate dominants were Ascomycota (84%) in the Technosol and Basidiomycota (89%) in the Phaeozem. Three phyla (Proteobacteria, Acidobacteria and Actinobacteria), together comprising more than a half of the bacteriobiome, prevailed in both soils; however, at the OTU level, soil-related differences were found for 31% of the OTUs. The Technosol bacteriobiome was less structured and more diverse compared to the mycobiome, displaying the same phylum-level structure and OTU-based α-biodiversity as in the adjacent mature soil. Our finding that few fungal and bacterial OTUs dominated in the soil microbiome, the majority being minor or rare members, implies that key ecosystem processes performed by soil microorganisms rely on a very limited taxonomic diversity, both in young and mature soils.