Community dynamics of ammonia oxidizing bacteria in a full-scale wastewater treatment system with nitrification stability

To determine whether the functional stability of nitrification was correlated to a stable community structure of ammonia oxidizing bacteria (AOB) in a full-scale wastewater treatment plant, the AOB community dynamics in a wastewater treatment system was monitored over one year. The community dynamics were investigated using specific PCR followed by terminal restriction fragment length polymorphism (T-RFLP) analysis of the amoA gene. The T-RFLP results indicated that during the period of nitrification stability, the AOB community structure in the full-scale wastewater treatment system was relatively stable, and the average change rate every 15 d of the system was 6.6%±5.8%. The phylogenetic analysis of the cloned amoA gene showed clearly that the dominant AOB in the system was Nitrosomonas spp. The results of this study indicated that throughout the study period, the AOB community structure was relatively stable in the full-scale wastewater treatment system with functional stability of nitrification.     

环境微生物群落分析的T-RFLP技术及其优化措施

末端限制性酶切片段长度多态性分析(terminal restriction fragment length polymorphism, T-RFLP)是近年来发展起来的、不依赖于培养的微生物群落分析方法之一.由于其在微生物群落结构分析方面的特点,包括分辨率高、易于实现自动化及互联网海量数据共享等优势,自1997年最先被报道以来得到了广泛的应用,成为环境微生物群落分析的最强有力的工具之一.本文详细介绍了T-RFLP技术的原理,并从环境样品群落DNA的提取、引物设计和PCR扩增、限制性酶切、电泳分离检测和T-RFLP图谱解析等5个方面讨论了用该技术解析环境微生物群落的方法和技巧,简述了近8 a来国外T-RFLP技术在群落分析中的研究进展.类似于其他的分子微生物生态学技术, T-RFLP也有自身的缺陷,因此重点分析了该技术的局限性及相应的解决办法.图2表1参62     

Microbial activity and accumulation of organic matter in the burrow of the mud shrimp, <Emphasis Type="Italic">Upogebia major</Emphasis> (Crustacea: Thalassinidea)

Microbial activity and accumulation of organic matter in the burrow of the thalassinidean mud shrimp, Upogebia major, were studied on a tidal flat along the northern coast of Tokyo Bay, Japan. The burrow of U. major is Y-shaped with an upper U-shaped part plus a lower I-shaped part. Its lower part can extend to a depth of 2 m. In the present study, we compare electron transport system activity (ETSA), bacterial abundance and organic matter content [total organic carbon (TOC), total nitrogen (TN) and chlorophyll a (chl. a)] of the burrow wall sediment with the tidal flat surface and non-burrow sediments. We also compared the U- and I-shaped part in terms of these parameters. ETSA in the burrow wall was higher than at the tidal flat surface in the warmer season, and was always higher than at surrounding non-burrow sediments. Bacterial abundance in the burrow wall was higher than at the tidal flat surface and surrounding sediment. TOC and TN contents in the burrow wall were two to three times higher than those at the tidal flat surface and non-burrow sediments, regardless of season. However, there was no significant difference in chl. a content between burrow wall and tidal flat surface. These results suggest that organic enrichment of the burrow wall is a result of organic matter particles such as phytodebris accumulation along the burrow wall. For all parameters of the burrow walls, no statistical differences were found between the two parts. Present results indicate that U. major actively transports the water containing suspended organic particles not only through the U-part but also into the deeper I-part. These indicate that burrow of the mud shrimp provides a dynamic environment for microbial community in tidal flat sediment.     

厦门冬季PM_（2.5）颗粒物中细菌和真核微型生物群落组成及其来源分析

近年来由于雾霾事件频发,有关细颗粒物PM2.5的来源、组成及迁移转化规律已经引起了人们的广泛关注,然而对于PM2.5颗粒物中微生物的组成和来源还知之甚少。本文应用T–RFLP、克隆文库和测序方法研究厦门2012年冬季PM2.5颗粒物中细菌和真核微型生物的群落组成,并分析其潜在的来源环境。研究结果表明：与克隆文库方法相比,T–RFLP分析所得的物种数量（TRF峰）相对较多,说明T–RFLP是快速、灵敏分析空气微生物群落特征的高效手段之一。T–RFLP和克隆文库结果表明,PM2.5颗粒物中细菌和真核微型生物群落多样性较高,其中2%的细菌16S rRNA基因和42%的真核微型生物18S rRNA基因序列与已知序列的相似度低于97%。分类分析表明,Bacteroidetes、Actinobacteria、Firmicutes和Proteobacteria是PM2.5颗粒物细菌的主要类群,其相对丰度分别为2.91%、10.68%、41.75%和44.66%;Stramenopiles、Alveolata、Metazoa、Fungi和Viridiplantae是PM2.5颗粒物真核微型生物的主要类群,其相对丰度分别为5%、7%、15%、20%和39%。然而,尚有14%的真核微型生物18S rRNA基因序列未能分类到已知门类,说明气溶胶真核微型生物方面的研究尚存在较大空白。与文献对比分析表明,厦门城区空气微生物的动态性较强,环境来源多变。环境来源分析表明,厦门虽然属于典型海滨城市,但其空气微生物的重要环境源可能为淡水,其次是土壤、水体沉积物、污水系统和动物粪便等。而季节性气团输送可能是厦门冬季气溶胶微生物多来源于淡水的原因之一。     

北运河水体浮游细菌群落的空间分布特征及其与水质的关系

污染源汇入和闸坝拦截等因素能够影响城市河流水生生态环境质量,主要表现在群落结构和功能的改变。分别于春季、夏季和冬季3个季节对北运河干流的10个点进行水样采集,通过16S rDNA末端限制性片段长度多态性(T-RFLP)分析手段研究了北运河河道水体浮游细菌的群落结构,以揭示流域微生物多样性以及浮游细菌群落与水质因子的响应关系。共得到47种不同的片段,其中218bp片段是优势菌。T-RFs片段计算微生物多样性指数和均匀度指数结果表明,目前北运河水体生态结构已经较为脆弱。冬季与其他季节的群落组成有明显差别,夏季细菌丰度高于冬季。通过CANOCO软件分析浮游细菌群落结构与水质指标的空间特点,发现水体流动性降低、支流汇入和污染源的汇入都会引起微生物群落结构在空间上的改变;环境因子与微生物群落组成的相关性研究表明,总磷、溶解性有机碳(DOC)和温度对北运河微生物群落结构影响较大。     

Genetic stock structure of the swordfish (Xiphias gladius ) inferred by PCR-RFLP analysis of the mitochondrial DNA control region

Restriction fragment length polymorphism (RFLP) analysis was performed on PCR amplified DNA fragments containing the control region of the swordfish (Xiphias gladius Linnaeus, 1758) mitochondrial DNA. A total of 456 individuals comprising 13 local samples (six Pacific, three Atlantic, the Mediterranean Sea, two Indian Ocean and the Cape of Good Hope) were surveyed with four endonucleases (Alu I, Dde I, Hha I and Rsa I), yielding a total of 52 composite genotypes. Within-sample genotypic diversity (H) was high ranging from 0.702 to 0.962 with a value of 0.922 for the pooled sample. Significant geographic variation in the frequencies of genotypes and restriction patterns was revealed. The Mediterranean sample was highly distinct from all other samples. Further, Rsa I digestion revealed high levels of polymorphism in all but the Mediterranean samples, indicating that exogenous swordfishes rarely enter that body of water. Heterogeneity between the North and South Atlantic samples was significant, both of which differed from those of the Pacific. In contrast, the Indian Ocean samples were not significantly different from the samples of South Atlantic and Pacific. Genetic differentiation among the Pacific samples was low. The results indicate that the world-wide swordfish population is genetically structured not only among, but also within ocean basins and suggest that gene flow is restricted despite the absence of geographic barriers. Received: 28 August 1996 / Accepted: 2 October 1996     

The ecology of the molluscs of Thalassia communities,Jamaica, West Indies. II. Molluscan population variability along an environmental stress gradient

Along a composite onshore-offshore gradient, 4 homogeneous areas within beds of the marine angiosperm Thalassia were studied in detail. Eleven environmental variables, and molluscan and echinoderm abundance were sampled at monthly intervals for 1 year. Environmental conditions were generally more extreme, and their variance greatest, nearshore; they decreased significantly with distance from shore. Environmental predictability and cumulative diversity (H) increased with distance from shore, whereas abundance was greatest in the higher-stress environments. Over the year, the population variance (number of species, density, and diversity) was no greater in the unpredictable, low diversity environments than in the more predictable, high-diversity environments. Bivalves collected from the low-diversity environments were markedly eurytopic forms. whereas the highest-diversity area contained predominantly stenotopic taxa. Typical suspension feeders were dominant only in the most diverse area, whereas more generalized feeders dominated the higher-stress environments. There was no correlation between bivalve diversity increased with the variety of available food. Evidence suggests that catastrophes and other long-term phenomena, and biological factors such as predation, are of great importance in determining the differences in fauna between these areas.     

Landbased Pollution Sources and Marine Environmental Quality in the Caribbean

Abstract

The near shore coastal and marine environment of several Caribbean islands is their most biologically productive and economically important zone. However, almost all landbased activities possess the real potential of degrading the quality of near shore waters and ultimately diminishing the utility of the marine resource. This condition is largely attributed to the individual smallness of the islands and their geographic proximity to each other.

Available sanitary water quality data from across the region indicated that while recreational areas are in general safe for water contact activities, bacterial densities in excess of several international criteria are consistently recorded in harbours. Organochlorine pesticide residues were generally in the 5 ng l^?1 range in unfiltered sea water but were significantly higher (1–100) ng g^?1 in limited samples of sediment and biota. Additional data requirements to gain further insight into the current state of the Caribbean environment are also identified.

A summary of the major land based sources of marine pollution (including sewage, industrial effluents and agricultural run-off) in the insular Caribbean is presented.     

炼油厂周边PAHs污染土壤中微生物群落结构多样性研究

直接从污染土壤中提取微生物基因组DNA,对基因组DNA进行16S rDNA聚合酶链式反应（PCR）扩增和末端限制性片段多态性（T-RFLP）分析,进而对炼油厂附近PAHs污染区土壤微生物群落结构和多样性进行初步研究。结果表明,PAHs浓度较高的土壤中PAHs主要以高相对分子质量PAHs为主,此外,其土壤微生物群落多样性明显低于PAHs浓度较低的土壤。高浓度PAHs刺激了某些土壤微生物生长。不同污染程度的土壤存在一定数量相同的优势菌群,但相对丰度具有明显差异。其中α-变形菌是五个区域土壤中的主导微生物。研究结果将为炼油厂周边土壤的修复治理提供科学依据。     

Factors affecting enumeration and isolation of actinomycetes from Chesapeake Bay and Southeastern Atlantic Ocean sediments

Studies of the seasonal distribution of heterotrophic bacteria in Chesapeake Bay (USA) led us to the observation that fungizone was selective for actinomycetes without appreciably altering the total viable aerobic, heterotrophic bacterial counts. A study of the actinomycete populations in the Bay was undertaken, with several media compared for ability to enrich for actinomycetes: basal, casein, Czapek, starch-casein, glycerol-glycine, chitin and oil agar No. 2. Between 40 and 100% of the colonies appearing on chitin and oil No. 2 media were found to be actinomycetes, compared with <2% for the other media employed. It was also found that if sediment samples are frozen, a practice followed when laboratory facilities are not available in the field, a decrease in the total counts and in the actinomycete colony counts occurred. However, on a proportional basis, a slight increase in the percent actinomycetes was noted. A minimum of 21 days incubation time is recommended for recovery of actinomycetes. Also, the absence of NaCl from the actinomycete isolation media and incubation temperatures ≥15°C should give good recoveries of actinomycetes. A seasonal distribution of actinomycetes was noted for Chesapeake Bay, with maximal populations of actinomycetes observed in March and November. Actinomycetes were isolated in the ocean from depths ranging from 7 to 7,790 m. Greater numbers of actinomycetes were isolated using an incubation temperature of 25°C for the estuarine stations and 15°C for the deep-ocean stations. Greater numbers of actinomycetes were associated with polluted environments close to shore.     

A general bioeconomic simulation model for annual-crop marine fisheries

A generalized bioeconomic simulation model of annual-crop marine fisheries is described and its use in marine fisheries management is demonstrated. The biological submodel represents the recruitment of new organisms into the fishery, the movement of organisms from one fishing area to another and from one depth to another, the growth of organisms and the mortality of organisms resulting both from natural causes and from fishing. The economic submodel represents the fishing effort exerted on each resource species, the monetary costs of fishing, the value of the harvest and the rent (or excess profits) to the fishery.Basic dynamics of the model results from changes in the number of organisms in the fishery over time, which can be summarized as a set of difference equations of the general form ΔN/Δt = R + I ? E ? M ? F where ΔN/Δt is the net change in number of organisms in the fishery over time, R is recruitment, I is immigration, E is emigration, M is natural mortality and F is fishing mortality. R is a driving variable, whereas I, E, M and F are functions of the state of the system at any given point in time. The model can be run in a deterministic or stochastic mode. Values for parameters affecting rates of recruitment, movement, growth, natural mortality and fishing mortality can be selected from uniform, triangular or normal distributions.Use of the model within a fisheries-management framework is demonstrated by evaluating several management alternatives for the pink shrimp (Penaeus duorarum) fishery on the Tortugas grounds in the Gulf of Mexico. Steps involved in use of the model, including parameterization, validation, sensitivity analysis and stochastic simulations of management policies, are explained.     

Dynamic intra-seasonal habitat use by Antarctic fur seals suggests migratory hotspots near the Antarctic Peninsula

Antarctic fur seals (Arctocephalus gazella) are major secondary consumers in the Southern Ocean, placing them in potential competition with commercial fisheries and requiring research to understand their seasonal habitat use. Using the data obtained during 14 shipboard surveys sampled on a fixed grid (150 K km²) during mid- to late summer, I quantified the spatial distribution and intra-seasonal variability of fur seal sightings relative to distance to land and hydrographic boundaries. I test the hypothesis that fur seals display an increase in their at-sea abundance during mid- to late summer near the Antarctic Peninsula as they prepare to take up wintering grounds. I also test whether abundances of their potential prey, krill and myctophids, exhibit intra-seasonal variability. During midsummer, high-abundance areas are located near major breeding colonies; however, during late summer, there is an order-of-magnitude increase in fur seal abundance, coinciding with an increase in the number of high-abundance areas located in Bransfield Strait. Coincidently, abundance of Euphausia superba decreased and the myctophid Electrona antarctica increased between mid- and late-summer surveys. High-abundance areas of fur seals are not associated with the southern Antarctic Circumpolar Current front but are concentrated within 100 km from land, potentially indicating the location of haul out and important coastal habitat use areas. The dynamic increase in the number and location of high-abundance areas during late summer represents a considerable amount of mammalian predators entering the Antarctic Peninsula marine ecosystem. This information is important for understanding the seasonal impact of fur seals on regional marine food webs and their potential interaction with the autumn–winter krill fishery.     

Methanogenic community structure in simultaneous methanogenesis and denitrification granular sludge

A laboratory scale up-flow anaerobic sludge bed (UASB) bioreactor fed with synthetic wastewater was operated with simultaneous methanogenesis and denitrification (SMD) granules for 235 days with a gradient decrease of C/N. Molecular cloning, qRT-PCR and T-RFLP were applied to study the methanogenic community structures in SMD granules and their changes in response to changing influent C/N. The results indicate that when C/N was 20:1, the methane production rate was fastest, and Methanosaetaceae and Methanobacteriaceae were the primary methanogens within the Archaea. The richness and evenness of methanogenic bacteria was best with the highest T-RFLP diversity index of 1.627 in the six granular sludge samples. When C/N was reduced from 20:1 to 5:1, the methanogenic activity of SMD granules decreased gradually, and the relative quantities of methanogens decreased from 36.5% to 10.9%. The abundance of Methanosaetaceae in Archaea increased from 64.5% to 84.2%, while that of Methanobacteriaceae decreased from 18.6% to 11.8%, and the richness and evenness of methanogens decreased along with the T-RFLP diversity index to 1.155, suggesting that the community structure reflected the succession to an unstable condition represented by high nitrate concentrations.

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Substrate-dependent bacterivory by intertidal benthic copepods

The trophic importance of bacteria to harpacticoid copepods in intertidal areas remains poorly understood, and so do the mechanisms of bacterial feeding. It is, for instance, unclear whether harpacticoids directly target bacterial cells or merely co-ingest them with substrates to which bacterial cells may be attached. Here, we investigate bacterial uptake and substrate requirement for four mud intertidal species (Microarthridion littorale, Platychelipus littoralis, Delavalia palustris and Nannopus palustris) by means of ¹³C-labeled bacteria and biomarker fatty acids (FA). Bacterial uptake strongly depended on grazing on a primary food source but bacterial ingestion rates were low, and no clear indication of copepods directly targeting bacteria was found. Delavalia was the only species that accumulated bacteria-derived FA and gained in polyunsaturated FA (PUFA) probably through bioconversion of bacteria-derived FA. In general, however, our results suggest that bacteria represent a relatively minor and low-quality food for intertidal harpacticoid copepods.     

How an introduced seaweed can affect epibiota diversity in different coastal systems

Invasions by non-indigenous species have the potential to alter the biodiversity of recipient systems. The magnitude of this effect often depends on the nature of the invaded communities and the ecology of the invader. We investigated the impacts of the Japanese seaweed Sargassum muticum (Phaeophyceae, Fucales) on biodiversity in a rocky and sedimentary environment on two islands in the North Sea. In each case, we compared the epibiota of non-indigenous S. muticum with epibiota communities on taxonomically related and structurally similar native seaweed hosts. Total and average species richness on S. muticum were similar on the rocky shore (60 species and 22±6 species, respectively) and the sandy shore (64 species and 20±3 species, respectively). However, community structure and species composition differed significantly between the environments. On the rocky shore, another native fucoid seaweed, Halidrys siliquosa, supported an epibiota community very similar to that of the invader. On the sandy shore, the only other abundant native habitat-providing algal species was Fucus vesiculosus. This species supported a different and less diverse assemblage of associated taxa. We conclude that S. muticum enhances epibiota diversity in the sedimentary environment, probably by increasing the substratum availability and habitat heterogeneity. In contrast, it has negligible impacts on epibiota diversity in the rocky shore environment, where it does not represent a fundamentally new habitat component. We conclude that even within the same region, the consequences of non-indigenous species on biodiversity cannot be generalised but depend on the composition and structural complexity of the species in the recipient community. This paper is dedicated to Udo Schilling, Chief Diving Officer, Alfred Wegener Institute who trained all of the authors in the waters off Helgoland to be scientific divers. The work reported here and in previous publications has been made possible through Udo’s training and support. We remain grateful for his enthusiasm, effort and patience.     

Diversity and community composition of phosphorus accumulating organisms (PAOs) in the sediments of the Sanshiliujiao Lake reservoir北大核心CSCD

The diversity and community composition of phosphorus accumulating organisms (PAOs) in the sediments of the Sanshiliujiao Lake reservoir in Pingtan island, Fujian Province, were investigated by terminal restriction fragment length polymorphism (T-RFLP) methods combined with the construction of clone libraries. The diversity of PAOs in summer samples was significantly higher than that in winter. The dominant terminal restriction fragments (T-RFs) of PAOs were in the range of 200 to 300 bp in summer, while they were in the range of 150 to 200 bp in winter. Cloning sequencing and phylogenetic analysis showed that the main phyla of PAOs in the sediment of the Sanshiliujiao Lake reservoir were Proteobacteria, Actinobacteria, and Acidobacteria. Anaeromyxobacter, Azospirillum, Microlunatus phosphovorus, and Burkholderia were the dominant genera in the summer samples. Anaeromyxobacter, Methylobacterium, Solibacter, Azospirillum, and Microlunatus phosphovorus were the dominant genera in sediment samples in winter. The results of this study demonstrated that the diversity and community composition of PAOs in the sediments of the Sanshiliujiao Lake reservoir had specific seasonal characteristics. Various forms of phosphorus also showed their influence on the diversity of PAOs, especially Fe/Al-P. Our findings lays a scientific foundation for the future disclosure of microbial mechanisms involved in the phosphorus metabolic cycle in the sediments of reservoirs. © 2018 Science Press. All rights reserved.     

Response of bacterial communities to short-term pyrene exposure in red soil

Pyrene, a representative polycyclic aromatic hydrocarbon (PAH) compound produced mainly from incomplete combustion of fossil fuels, is hazardous to ecosystem health. However, long-term exposure studies did not detect any significant effects of pyrene on soil microorganism. In this study, short-term microcosm experiments were conducted to identify the immediate effect of pyrene on soil bacterial communities. A freshly-collected pristine red soil was spiked with pyrene at 0, 10, 100, 200, and 500 mg·kg^-1 and incubated for one day and seven days. The bacterial communities in the incubated soils were analyzed using 16S rRNA sequencing and terminal restriction fragment length polymorphism (T-RFLP) methods. The results revealed high bacterial diversity in both unspiked and pyrene-spiked soils. Only at the highest pyrene-spiking rate of 500 mg·kg^-1, two minor bacteria groups of the identified 14 most abundant bacteria groups were completely suppressed. Short-term exposure to pyrene resulted in dominance of Proteobacteria in soil, followed by Acidobacteria, Firmutes, and Bacteroidetes. Our findings showed that bacterial community structure did respond to the presence of pyrene but recovered rapidly from the perturbation. The intensity of impact and the rate of recovery showed some pyrene dosage-dependent trends. Our results revealed that different levels of pyrene may affect the bacterial community structure by suppressing or selecting certain groups of bacteria. It was also found that the bacterial community was most susceptible to pyrene within one day of the chemical addition.     

Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium

The aim of this study is to analyze the effect of salinity on polycyclic aromatic hydrocarbons (PAHs) biodegradation, community structure and naphthalene dioxygenase gene (ndo) diversity of a halophilic bacterial consortium with the denaturing gradient gel electrophoresis (DGGE) approach. The consortium was developed from oil-contaminated saline soil after enrichment for six times, using phenanthrene as the substrate. The prominent species in the bacterial consortium at all salinities were identified as halophilic bacteria Halomonas, Alcanivorax, Marinobacter, Idiomarina, Martelella and uncultured bacteria. The predominant microbes gradually changed associating with the saline concentration fluctuations ranging from 0.1% to 25% (w/v). Two ndo alpha subunits were dominant at salinities ranging from 0.1% to 20%, while not been clearly detected at 25% salinity. Consistently, the biodegradation occurred at salinities ranging from 0.1% to 20%, while no at 25% salinity, suggesting the two ndo genes played an important role in the degradation. The phylogenetic analysis revealed that both of the two ndo alpha subunits were related to the classic nah-like gene from Pseudomonas stutzeri AN10 and Pseudomonas aeruginosa PaK1, while one with identity of about 82% and the other one with identity of 90% at amino acid sequence level. We concluded that salinity greatly affected halophilic bacterial community structure and also the functional genes which were more related to biodegradation.

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Recovery of benthic communities at Macquarie Island (sub-Antarctic) following a small oil spill

Intertidal communities at Macquarie Island (sub-Antarctic) were re-evaluated seven years after a small oil spill resulting from the grounding of the “Nella Dan”, and six years after the first assessment of biological impact. Sampling was conducted to evaluate community structure in three zones of the exposed rocky shore (upper red, kelp, and lower red) and in samples of Durvillaea antarctica holdfasts. There were no significant differences between the community structure in oiled and control locations in any of the three shore zones, but holdfast macrofaunal communities at oiled sites still showed evidence of impact. Holdfast community-structure in samples from heavily oiled sites showed moderate levels of recovery, with increased abundances of species which were considered sensitive to the oiling in the first post-impact studies and decreased abundances of opportunistic polychaete and oligochaete worms. In contrast, samples collected from the moderately oiled location at Secluded Bay showed little evidence of recovery. Holdfasts at this site were filled with sediment containing traces of diesel oil, and the macrofaunal community was dominated by opportunistic worms. This study clearly indicates that even small incidents of anthropogenic perturbation can have long-lasting consequences for marine communities at Macquarie Island. Received: 23 July 1997 / Accepted: 5 February 1998