Molecular characterization of bacterial communities associated with sediments in the Laurentian Great Lakes

The Laurentian Great Lakes freshwater ecosystem comprises a series of interconnected lakes exhibiting wide spatial differences in hydrogeochemistry, productivity, and allochthonous inputs of nutrients and xenobiotics. Bacterial communities associated with offshore sediments in this ecosystem have been rarely studied. We evaluated bacterial communities associated with sediments from 10 locations in four of the five Great Lakes (Lakes Superior, Michigan, Huron, and Ontario) by generating16S rRNA pyrosequence libraries. Pyrosequencing analysis revealed the presence of 26 bacterial phyla and proteobacterial classes among Great Lakes sediment samples. Actinobacteria, Acidobacteria, Betaproteobacteria, and Gammaproteobacteria were the most abundant groups of bacteria. Redundancy analysis was used to examine the role of sediment properties, including depth and chemical composition, in shaping bacterial community structure. One sample from Lake Huron was distinctly different from all other samples. Phylogenetic analysis revealed that the sample contained greater abundances of groups of bacteria associated with polluted environments. This study constitutes the most extensive examination of bacteria associated with Laurentian Great Lakes sediments and sheds useful insight into the microbial ecology of the Great Lakes.     

多种修复技术对城市内河水质及微生物群落的影响

采集城市内河水样,分别采用曝气增氧、碳源添加、生物投菌和综合修复等技术,在实验室进行水质修复模拟实验,并以水质参数、微生物多样性及丰度为鉴定指标,分析不同修复技术对城市河流水质的修复效果及其对河流微生物群落结构的影响。结果表明,曝气、生物投菌和综合修复技术可以提高河流微生物群落结构多样性,水体微生物群落以变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteria)和疣微菌门(Verrucomicrobia)为主;而使用碳源添加技术的水样,河流微生物的多样性下降明显,变形菌门(Proteobacteria)的相对丰度达到了93%;水质修复方面,曝气增氧技术和生物投菌技术都仅能降低水体COD质量浓度,无法降低水体TN及NH+4-N质量浓度;碳源添加和综合修复技术,对水体TN和NH+4-N的去除效果明显,但投加碳源的河流水体中的COD质量浓度显著上升;相关性分析结果表明,影响水体微生物群落结构的主要环境因子为COD和DO。     

Watershed-scale landuse is associated with temporal and spatial compositional variation in Lake Michigan tributary bacterial communities

Populations of stream organisms across trophic levels, including microbial taxa, are adapted to physical and biotic stream features, and are sentinels of geological and hydrological landscape processes and anthropogenic disturbance. Stream bacterial diversity and composition can have profound effects on resident and migratory species in Great Lakes tributaries. Study objectives were to characterize and compare the taxonomic composition and diversity of bacterial communities in 18 rivers of the Lake Michigan basin during April and June 2019 and to quantify associations with stream and watershed physical features and dominant landuse practices. River water was filtered, and genomic DNA was extracted from filtrate using antiseptic techniques. We performed high-throughput amplicon sequencing using the highly variable V4 region of the 16S rRNA gene to characterize microbial community composition and diversity. Effects of landscape-scale landuse, environmental variables and dispersal predictors (e.g., inter-stream distance) on community compositional differences were quantified. Greater than 90% of variation in bacterial relative abundance between rivers and time were attributed to 11 phyla representing 10,800 operational taxonomic units. Inter-stream geographic distance, stream hydrology, and variation in stream properties that were tied to patterns of watershed landuse were significantly associated with differences in bacterial community composition among streams at both sampling time periods. based on Bray-Curtis distances. Understanding how environmental characteristics and watershed-scale landuse influence lower trophic level stream communities such as bacteria will inform managers as biological indicators of ecosystem health, sources of disturbance, and current and future bottom-up trophic changes in coupled tributary-Great Lakes ecosystems.     

Assessing Contamination in Great Lakes Sediments Using Benthic Invertebrate Communities and the Sediment Quality Triad Approach

Sediments in many Great Lakes harbors and tributary rivers are contaminated. As part of the USEPA's Assessment and Remediation of Contaminated Sediment (ARCS) program, a number of studies were conducted to determine the nature and extent of sediment contamination in Great Lakes Areas of Concern (AOC). This paper describes the composition of benthic invertebrate communities in contaminated sediments and is one in a series of papers describing studies conducted to evaluate sediment toxicity from three AOC's (Buffalo River, NY; Indiana Harbor, IN; Saginaw River, MI), as part of the ARCS Program. Oligochaeta (worms) and Chironomidae (midge) comprised over 90% of the benthic invertebrate numbers in samples collected from depositional areas. Worms and midge consisted of taxa identified as primarily contaminant tolerant organisms. Structural deformities of mouthparts in midge larvae were pronounced in many of the samples. Good concurrence was evident between measures of laboratory toxicity, sediment contaminant concentration, and benthic invertebrate community composition in extremely contaminated samples. However, in moderately contaminated samples, less concordance was observed between the benthos community composition and either laboratory toxicity test results or sediment contaminant concentration. Laboratory sediment toxicity tests may better identify chemical contamination in sediments than many commonly used measures of benthic invertebrate community composition. Benthic measures may also reflect other factors such as habitat alteration. Evaluation of non-contaminant factors are needed to better interpret the response of benthic invertebrates to sediment contamination.     

基于原生微生物MICP的土体加固试验研究

为研究原生微生物加固砂土的影响因素,进行了室内胶结试验。采用不同灌注方式和不同配比的溶液,对试样中原生脲酶微生物进行激活,待微生物分解尿素能力达到阈值后,鉴定试样中微生物种属并对其进行系统发育分析,然后开展微生物诱导碳酸钙沉淀(MICP)胶结试验。通过微生物浓度、尿素浓度来监测试样的生物化学变化,根据无侧限抗压强度(UCS)和扫描电子显微镜成像(SEM)来评估试样加固效果。试验结果表明:加固效果与胶结液的灌注方式、有机质浓度、尿素浓度关系密切,双向交替灌注有利于改善试样胶结的均匀程度,较高浓度的有机质(酵母提取物)对土体中微生物多样性产生不利影响,激活和胶结效果较差;使用0.35 mol/L尿素的试样残余尿素浓度较高,而使用0.20 mol/L尿素的试样中,尿素残余较少;此次研究中,采用双向交替灌注、1.0 g/L酵母提取物、0.20 mol/L尿素处理的试样,生成的碳酸钙晶体连接紧密,胶结程度较好,其UCS值达1.55 MPa。研究成果表明,使用一定配比的溶液,可激活土体中的原生微生物,达到加固土体的目的。     

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.     

Dynamic changes in environment condition and microbial community structure in trench and flat seabed sediments of Tokyo Bay, Japan.

Dynamic changes in the chemical environment in the bottom of overlying water and microbial community structure in trench and flat seabed sediments were evaluated during summer and autumn in Tokyo Bay, Japan, to elucidate the response of microbial community changes as a consequence of dredging activity. Quinone profile analysis was performed to evaluate the changes in microbial community structure in the sediments. Bottom shape and location of each station affected the chemical environment of the overlying water. The trench bottom shape had longer anoxic conditions than the flat bottom shape. Nitrogen and phosphorus concentrations affected the microbial density in the sediment. During anoxic conditions, the ubiquinone/menaquinone ratio (UQ/MK) was less than unity and increased with rising dissolved oxygen (DO) concentrations. The dominant quinone species in the trench and flat seabed sediments were MK with 6 and 7 isoprene units (MK-6 and MK-7) and UQ with 8 and 9 isoprene units (UQ-8 and UQ-9). MK-6 and UQ-8 containing bacteria might have a great influence on the sulfur cycle of the aquatic ecosystem. While, MK-7 and UQ-9 containing bacteria correlated with the deposition of phototropic bacteria cells onto the seabed sediment. The trench bottom shape contained higher concentrations of MK-6, MK-7, UQ-8 and UQ-9, especially during summer.     

豫东黄河故道湿地景观格局及其多样性变化

应用ERDAS遥感影像解译软件,在ArcGIS软件支持下建立了豫东黄河故道湿地景观要素数据库,采用景观多样性指数、斑块特征指数和分离度等指标,分析了豫东黄河故道湿地的景观格局多样性变化规律,以及影响其格局变化的驱动力。结果表明:从各景观多样性指数的变化看,丰富度、景观最大多样性指数和景观优势度均为低洼湿地带最大,说明该地带景观类型多样化;从斑块变化特征看,由低洼带到背脊带,斑块边界趋向复杂化,性状呈现不规则变化,且斑块面积有效性逐渐减弱,不利于物种保护和湿地生态价值、生态功能的提升。豫东黄河故道湿地演化的过程中,受到自然和人为两方面演化驱动力的共同作用,其中自然因素有黄河断流、促淤造陆和湿地自身演替变化等,人为驱动力主要有农田开垦、滩涂开发及人工建筑等。     

水生植物对沉积物微生物群落功能多样性的影响

为研究水生植物对沉积物微生物群落功能多样性的影响,采用Biolog-Eco微平板法分析非根际沉积物及菖蒲根际沉积物微生物群落功能多样性差异。结果表明:水生植物菖蒲的生长可大大提高沉积物中微生物的活性及多样性,菖蒲根际微生物总活性(AWCD)、微生物多样性指数(包括Shannon-Wiener 指数、丰富度指数及Pielou 均匀度指数)均显著高于非根际沉积物。菖蒲根际沉积物微生物主要是一些利用酯类及糖类作为碳源的微生物类群,而非根际沉积物微生物主要利用酯类及胺类碳源。菖蒲根际沉积物及非根际沉积物之间的代谢差异的碳源主要有D-纤维二糖、β-甲基D-葡萄糖苷、葡萄糖-1-磷酸、D-半乳糖醛酸及D-葡萄胺酸、苯乙基胺、N-乙酰基-D-葡萄胺、D-半乳糖内酯、D-甘露醇及D,L-a-甘油。根际及非根际微生物群落功能多样性差异可为揭示水生植物对水环境沉积物的根际效应机制提供一定的科学依据。     

Analysis of nitrifying bacterial communities in aerobic biofilm reactors with different DO conditions using molecular techniques

In order to assess the relationship between the dissolved oxygen (DO) concentration and the characteristics of nitrifying bacterial communities in an aerobic biofilm reactor, molecular techniques including denaturing gradient gel electrophoresis (DGGE)/cloning based on PCR targeting 16S rRNA and the amoA gene and fluorescence in situ hybridisation (FISH) were conducted. The D-1, D-2, D-3 and D-4 reactors with different DO concentrations (1, 3, 5 and 7 mg/L, respectively) were set up in the thermostat and acclimated. The optimal DO concentration with stable nitrification efficiency was above 5.0 mg/L. As was shown by the results of DGGE and cloning, the community of ammonia-oxidising bacteria (AOB) and the ratio of Nitrosomonas sp. changed only slightly despite their differing nitrification efficiencies. The results of FISH indicated that higher DO concentrations resulted in an increase in AOB and nitrite-oxidising bacteria (NOB), and a reduction in heterotrophic microorganisms. The INT-dehydrogenase activity (DHA) test demonstrated that the activity of AOB decreased with reductions in the DO concentration. This means that the DO concentration does not influence the community of AOB, but rather the activity of AOB. In the relationship between the attached biomass and the nitrification efficiency, only the active biomass affected the nitrification efficiencies.     

Assessing the impacts of light synthetic crude oil on microbial communities within Laurentian Great Lakes’ sediment habitats

The ability of microbial communities to respond to and degrade crude oil in marine environments is well understood, yet fewer studies have examined freshwater environments. The Laurentian Great Lakes are one of the world’s largest surface freshwater sources. A pipeline that transports light synthetic crude oil crosses between two of the Great Lakes (the Straits of Mackinac, connecting Lakes Michigan and Huron, U.S.A.), and there is uncertainty on how the various habitats within this region would respond to accidental crude oil exposure. In this study, sediment microbial communities from three distinct habitats (coastal beach, freshwater coastal wetland, and Lake Michigan deep sediments) were used in microcosm experiments to document their community response (16S rRNA gene sequencing) to light synthetic crude oil (headspace gas chromatography). Microbial community structure (beta diversity) was impacted after exposure to crude oil in each of the habitats examined, with each habitat showing a different level of resistance to crude oil. Additionally, within each habitat, beta diversity distinguished sub-communities that increased in abundance in experimental treatments. Specifically, an increase in total abundance of Alphaproteobacteria, Betaproteobacteria, or Gammaproteobacteria was observed in microcosms exposed to crude oil regardless of habitat type. Methane, a potential hydrocarbon degradation byproduct, was observed in the headspace of the microcosms after exposure to crude oil, which may indicate methanogenic hydrocarbon degradation. These data suggest Great Lakes freshwater microbial communities will respond differently to crude oil exposure but may have shared community members involved in resisting and degrading light synthetic crude oil.     

Microbial community of biological phosphorus removal process fed with municipal wastewater under different electron acceptor conditions.

The microbial community in a biological phosphorus removal process under different electron acceptor conditions was estimated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay and principal-component analysis (PCA). For this purpose, a lab-scale sequencing batch reactor (SBR) fed with municipal wastewater was operated under anaerobic-aerobic, anaerobic-anoxic-aerobic and anaerobic-anoxic conditions. The results of PCR-DGGE targeting the 16S rRNA gene indicated a significant shift in the microbial community with electron acceptor conditions. From the 16S rRNA-based PCA, the microbial shift implies that little oxygen supply caused the deterioration of aerobic bacteria, including aerobic polyphosphate-accumulating organisms (PAOs). Moreover, it also reflects the existence of nitrate-utilizing denitrifiers. On the other hand, although the band patterns of DGGE targeting a functional gene of denitrification (nirS) also showed the microbial shift, the result of PCA differed from that of 16S rRNA-based analysis. There is no conclusive proof that the bacteria represented as the dominant bands detected in the present study are denitrifying-PAOs so far, it should be worthwhile to identify the detected bacteria and to examine their traits as new denitrifying-PAO candidates.     

Benthic Community and Sediment Quality Assessment of Port Hope Harbour,Lake Ontario

Sediments in Port Hope Harbour, Lake Ontario, have been heavily contaminated by radionuclides and heavy metals from a radium recovery plant, a uranium refinery, and other industrial activities. Spatial patterns in surficial sediment contamination, benthic community structure, and bioaccumulation of contaminants were assessed to determine possible relationships and potential environmental hazards in the event of dredging. Benthic community differences in species composition and density between inner and outer harbour areas corresponded with both habitat and sediment quality differences. Sediment loss-on-ignition, nitrogen, iron, copper, lead, chromium, zinc, and nickel concentrations in the inner harbour exceeded provincial guidelines for open water disposal of dredged spoils. Only iron exceeded those guidelines in the outer harbour. Tissue levels of radionuclides and heavy metals in benthic invertebrates were greatest at the most heavily contaminated stations in the inner harbour. Reduced benthic densities and maximum sediment contamination occurred near a refinery cooling water discharge.     

Performance and microbial ecology of the hybrid membrane biofilm process for concurrent nitrification and denitrification of wastewater.

We report on a novel process for total nitrogen (TN) removal, the hybrid membrane biofilm process (HMBP). The HMBP uses air-supplying hollow-fibre membranes inside an activated sludge tank, with suppressed aeration, to allow concurrent nitrification and denitrification. We hypothesised that a nitrifying biofilm would form on the membranes, and that the low bulk-liquid BOD concentrations would encourage heterotrophic denitrifying bacteria to grow in suspension. A nitrifying biofilm was initially established by supplying an influent ammonia concentration of 20 mgN/L. Subsequently, 120 mg/L acetate was added to the influent as BOD. With a bulk-liquid SRT of only 5 days, nitrification rates were 0.85 gN/m(2) per day and the TN removal reached 75%. The biofilm thickness was approximately 500 lim. We used DGGE to obtain a microbial community fingerprint of suspended and attached growth, and prepared a clone library. The DGGE results, along with the clone library and operating data, suggest that nitrifying bacteria were primarily attached to the membranes, while heterotrophic bacteria were predominant in the bulk liquid. Our results demonstrate that the HMBP is effective for TN removal, achieving high levels of nitrification with a low bulk-liquid SRT and concurrently denitrifying with BOD as the sole electron donor.     

Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA gene

The diversity of bacterial groups in activated sludge from large- and small-scale wastewater treatment plants was explored by barcoded pyrosequencing of 16S rRNA gene. Activated sludge samples (three small and 17 large scale) were collected from 12 wastewater treatment plants to clarify precise taxonomy and relative abundances. DNA was extracted, and amplified by 4 base barcoded 27f/519r primer set. The 454 Titanium (Roche) pyrosequences were obtained and analyses performed by Quantitative Insight Into Microbial Ecology (QIIME) with around 100,000 reads. Sequence statistics were computed, while constructing a phylogenetic tree and heatmap. Computed results explained total microbial diversity at phylum and class level and resolution was further extended to Operational Taxonomic Unit (OTU) based taxonomic assignment for investigating community distribution based on individual sample. Composition of sequence reads were compared and microbial community structures for large- and small-scale treatment plants were identified as major phyla (Proteobacteria and Bacteroidetes) and classes (Betaproteobacteria and Bacteroidetes). Also, family level breakdowns were explained and differences in family Nitrospiraceae and phylum Actinobacteria found at their species level were also illustrated. Thus, the pyrosequencing method provides high resolution insight into microbial community structures in activated sludge that might have been unnoticed with conventional approaches.     

Mesocosm observations on the ecological response of an aquatic community to sediment contamination

Between 1992 and 1997 the effects of contaminated sediment on an aquatic community were studied in outdoor mesocosms (2m³), one filled with ‘naturally’ polluted sediment from the sedimentation area ‘Ketelmeer’, the other with relatively clean sediment from the shallow lake ‘Oostvaardersplassen’. Negative effects of the contaminated sediment were observed on the population development of the amoeba species Arcella megastoma and Diflugia accuminata, the mysid shrimp Neomysis integer, the microlepidopteran Cataclysta lemnata and the cladoceran community, whereas the biting midge Culex sp. showed a preference for the contaminated system. The reduction of the grazing capacity of the cladoceran community resulted in higher algal densities in the ‘Ketelmeer’ mesocosm despite the fact that nutrient concentrations in the water column of both mesocosms were comparable.     

长距离输水过程中微生物安全的分子生物学分析

应用PCR-DGGE分子生物学方法对东江水源工程沿途水样中的微生物群落结构的动态变化以及种群多样性进行了研究。结果表明,采用分子生物学方法能够检测出水中多样性的细菌。相似性分析表明,采用涵管方式远距离引水,其沿途水中微生物群落结构变化并不是很大,优势菌大致相同;16SrDNA鉴定表明,分子生物学方法能够检测出传统人工培养方法不能检测出来的细菌,原水不含致病菌,这能够对原水输送工程微生物安全性进行更准确的评价。     

Identification of prevalent microbial communities in a municipal solid waste landfill.

To identify the microbial communities in Istanbul, Odayeri Municipal Solid Waste Landfill, leachate samples were collected from different sections at different stabilization phases. In identification of microbial communities in leachate samples, molecular techniques such as FISH, DGGE and cloning based on 16S rRNA and mcrA genes were used. As the chemical and microbiological compositions of the samples were compared, obvious correlations were found between the stability of the landfill section and abundance of active methanogens. On the other hand, there were considerable differences between acidogenic and mature leachate samples in DGGE profiles of archaeal and bacterial 16S rRNA genes. Moreover, in acidogenic leachate samples having BOD5/COD ratio of about 0.5 acetate utilizing Methanosarcina and Methanosaeta species were intensively detected in FISH. Although only very few H2-utilizing methanogens were identified with FISH analysis, most of the clones isolated from mature leachate samples clustered within H2-utilizing Methanobacteriales and Methanomicrobiales according to phylogenetic analysis of 16S rRNA and mcrA clones, respectively.     

Effects of low‐head dams on fish assemblages in subtropical streams: Context dependence on species category and data type

Anthropogenic disturbances may cause cosmopolitan species to replace endemic species, which will alter both the within‐community diversities and between‐community similarities of stream fish assemblages. In this study, we used data collected from headwater streams within the Xin'an basin, China, to evaluate the effects of low‐head dams on the alpha diversity and community similarity of fish assemblages. Our aims were to determine whether the changes in fish diversities and similarities related to dam‐associated disturbance are dependent on the species category (i.e., indigenous vs. native‐invasive species) or data type (i.e., occurrence‐based vs. abundance‐based indices). We found that low‐head dams significantly decreased the alpha diversity of the indigenous species in the impoundments but increased that of the native‐invasive species. However, the magnitude of this change was weakened if the two categories of fishes were not distinguished. Additionally, low‐head dams significantly decreased the occurrence‐based similarities of the indigenous fishes but increased those of the native‐invasive fishes. Despite the positive correlation between the occurrence‐based and abundance‐based indices, the former significantly overestimated the community similarities. Although most pairs of communities showed the same direction of changes for the two indices, some cases presented contrasting outcomes, including “perceived homogenization” (i.e., occurrence‐based differentiation but abundance‐based homogenization) and “perceived differentiation.” Our results suggest the importance of distinguishing indigenous and native‐invasive species and considering both occurrence‐based and abundance‐based indices in future research on how anthropogenic activities affect fish diversities and similarities in streams.