Influence of bacterial density on the exchange of phosphate between sediment and overlying water

Fluxes of phosphate across the sediment–water interface have been measured using inhibitors of bacterial activity sterilization and chloramphenicol and a control in order to quantify the influence of bacterial abundance on them. Results show that phosphate concentration in the interstitial water decreased when bacteria were present, in relation to treated aquaria. The measured (Jo) and theoretical fluxes (Jd) of phosphate also were higher when bacterial activity was suppressed. Mass balance calculated for Carbon, Nitrogen and Phosphorus in the sediment revealed a loss of theses compounds when bacterial activity was suppressed, and a net accumulation of Carbon and Phosphorus, and loss of Nitrogen under natural conditions.     

象山港网箱养殖区水体和沉积物的细菌生态分布

2006年1月和10月对象山港网箱养殖区细菌数量分布及群落结构进行研究,并与周边非养殖海域进行了比较。结果显示水体和沉积物细菌数量均呈现10月份1月份、网箱养殖区网箱外侧对照区近湾顶对照区近湾口对照区的分布特点,其中网箱养殖区水体异养细菌、弧菌数量分别在1.0×106—7.2×107CFU/L和1.6×105—1.3×106CFU/L之间,沉积物异养细菌、弧菌数量分别在5.9×102—6.1×105CFU/g和8.0×101—7.4×104CFU/g之间。网箱养殖区水体分离细菌89株,归属于12个属,其中不动杆菌属(Acinetobacter)、假单胞菌属(Pseudomonas)、弧菌属(Vibrio)等为优势菌属;沉积物分离细菌136株,归属于10个属,其中假单胞菌属(Pseudomonas)、弧菌属(Vibrio)、芽孢杆菌属(Bacillus)、不动杆菌属(Acinetobacter)等为优势菌属。由于长期受到高营养盐、高有机质等外界条件的选择作用,网箱区及网箱外侧对照区海域的细菌群落多样性较低,某些特定的细菌类群富集。研究表明网箱养殖区的细菌分布和菌属组成特征与养殖自身污染密切相关,并且养殖过程对细菌群落产生的影响已扩展至网箱外侧的邻近海域。     

The effects of nematodes on bacterial activity and abundance in a freshwater sediment

The effects of natural nematode communities on bacterial activity and abundance were investigated in a microcosm study. Nematodes were added at different densities to a freshwater sediment and bacterial parameters were measured after 1, 5, 9, and 17 days. Significant effects of nematode density on bacterial activity were noted on day 5. No long-term changes in bacterial activity were recorded. Bacterial abundance displayed an overall decrease in both treatments and controls. In a second experiment, the effect of nematode feeding-type on bacterial activity was studied. Microcosms were incubated with 100 individuals of a fungus-feeding (Aphelenchus avenae) or a bacteria-feeding nematode species (Caenorhabditis elegans) respectively, and bacterial activity was determined after 0, 1, 2, 4, and 7 days. Significant time and feeding-type effects were found, with consistently higher bacterial activity estimates in treatments with bacteria-feeding nematodes. These results suggest that grazing affects bacterial activity, and indicate that grazing by nematodes may be more important in stimulating bacterial activity than bioturbation or excretion. Combining these results, we conclude that natural nematode communities may have an impact on bacterial activity, and that the magnitude of this impact depends on the proportion of actively feeding bactivores within the community. Received: 2 September 1996 / Accepted: 20 May 1997     

Screening for microbial markers in Miocene sediment exposed during open-cast brown coal mining

Viable microorganisms were found in Miocene lacustrine clays of the cypris formation excavated from 200-m below the surface as spoil during open-cast brown coal mining (Sokolov Brown Coal Basin, North-Western Bohemia, Czech Republic). Both saprotrophic microfungi of the genera Penicillium, Verticillium, Cladosporium and Aspergillus as well as heterotrophic bacteria were isolated from an intact sediment cores. Heterotrophic bacteria were classified by the MIS Sherlock System as representatives of genera Nocardiopsis, Arthrobacter, Micrococcus, Kocuria, Rothia, Clavibacter, Bacillus, Paenibacillus, Brevibacillus, Microbacterium, Acinetobacter and Pseudomonas. A bacterium found among the strains had an atypical fatty acids profile enriched by branched fatty acids and polyunsaturated fatty acid (18:36) and gave no MIS Sherlock match. Phospholipid fatty acids analysis indicates a relatively high (535 pmol g⁻¹) but inhomogeneously distributed viable microbial biomass. Fatty acids analyses of non-fractioned lipids (representing viable, storage and dead biomass; 8390  pmol  g⁻¹) detected rich and homogenous profiles with fungal, bacterial and actinomycetal markers but no protozoan and algal fatty acids markers.     

Depth profile of sulfate-reducing bacterial ribosomal RNA and mercury methylation in an estuarine sediment

Abstract: The community structure of complex anaerobic microbial communities has been difficult to elucidate because of an inability to cultivate most of the contributing populations. In this study, the distribution of sulfate-reducing bacteria (SRB) in anaerobic sediments was determined using oligonucleotide probes complementary to the 16S ribosomal RNAs of major phylogenetic groups. Sediment cores were collected from Santa Rosa Sound in northwest Florida, and sectioned by depth into 1 to 2 cm fractions. Nucleic acids were extracted from each fraction and hybridized with the SRB-specific ribosomal RNA probes. SRB ribosomal RNAs accounted for almost 5% of the microbial community ribosomal RNA pool in the 3–4 cm depth fraction and were dominated by Desulfovibrionaceae ribosomal RNA. The SRB ribosomal RNA peak coincided with mercury methylation, an activity attributed to SRB. Profiles of the ribosomal RNAs indicate that SRB populations in sediments are stratified by depth.     

Spatio-Temporal Monitoring and Ecological Significance of Retrievable Pelagic Heterotrophic Bacteria in Kongsfjorden,an Arctic Fjord

Kongsfjorden is a glacial fjord in the Arctic that is influenced by both Atlantic and Arctic water masses. In the present report retrievable heterotrophic bacteria isolated from two distinct zones (outer and inner fjord) of Kongsfjorden was studied during summer to fall of 2012. 16S rRNA gene sequences of the retrievable heterotrophic bacteria corresponded to γ-proteobacteria (13 phylotypes), α-proteobacteria (3 phylotypes), Bacteroidetes (4 phylotypes) and Actinobacteria (2 phylotypes). The heterotrophic bacterial community structure was fundamentally different in different months which could be linked to changes in the water masses and/or phytoplankton bloom dynamics. It is hypothesized that monitoring the retrievable heterotrophic bacterial assemblage in the fjord would give valuable insights into the complex ecological role they play under extreme and dynamic conditions.     

Monitoring nutrient impact on bacterial community composition during bioremediation of anoxic PAH-contaminated sediment

Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.     

Heterotrophic bacterial activity and primary production in a hypertrophic African lake

The relationship between heterotrophic bacteria and phytoplankton in the epilimnion (0–10 m) of hypertrophic Hartbeespoort Dam, South Africa, was examined by statistically analyzing three years of parallel measurements of heterotrophic bacterial activity (glucose uptake) and phytoplankton particulate and dissolved organic carbon production. Algal biomass ranged between 4.0 and 921.1 mg Chl a m^-3 at the surface. Primary production varied between 69.5 and 3010.0 mg C m^-2h^-1 while algal production of dissolved organic carbon (EDOC) ranged from 2.5 to 219.2 mg C m^-2h^-1. Bacterial numbers reached a summer peak of 44.23 × 10⁶ cells ml^-1 in the first year and showed no depth variation. The maximum rate of glucose uptake, V_max, reached a peak of 5.52 g C l^-1h^-1. V_max, maximum glucose concentration (K_t + S_n) and glucose turnover time (T_t) were usually highest at the surface and decreased with depth concomitant with algal production. At the surface, V_max was correlated to EDOC (r = 0.59, n = 67, p < 0.001) and primary production (r = 0.71, n = 70, p < 0.001). At 5 and 10 m, V_max was correlated to integral euphotic zone (~ 4 m) algal production and bacterial numbers. Glucose turnover time was inversely related to integral algal production (r = -0.72, n = 70, p < 0.001) and less strongly to bacterial numbers. The data indicated that although bacterial numbers and biomass were low relative to algal biomass in this hypertrophic lake, the heterotrophic bacteria attained high rates of metabolic activity as a result of enhanced algal production of available organic carbon.     

Terminal electron transport system (ETS)-activity in the sediment of Lake Balaton,Hungary

Terminal electron transport system (ETS)-activity of the sediment and plankton of Lake Balaton, the largest shallow lake of Central Europe was measured by tetrazolium-reduction biweekly during 1989–1990 and in the spring of 1991. Sediment proved to be enzymatically active to 30-35 cm down in the hypertrophic Keszthely Bay and to 15–20 cm down in the meso-eutrophic Siófok Basin. Sediment ETS-activity exceeded planktonic activity 15 to 24 fold.The total activity m^–2 showed one or two order of magnitude higher respiratory potential in Lake Balaton than needed for complete oxidation of the planktonic primary production; most of this potential was detected in the upper 3–5 cm sediment layer in springs. Incubations of cell-free homogenates of sediment bacteria showed that ETS remains active days after death of organisms at low temperature. Accumulated postmortem ETS-activity derived from the benthic diatoms, bacteria, plankton deposit and dead summer macrophytes seems to be responsible for the high ETS-activity of the sediment in the warming periods in springs. These enzyme fractions may contribute to the rapid oxidation of the alkaline, well-aerated lake.     

Modulation of dissolved oxygen levels in a hypertidal estuary by sediment resuspension

Hyperconcentrated benthic layers, which form during neap tides, recruit much of the fine sediment population of the turbidity maximum of a hypertidal estuary. Measurements of tidal amplitude and suspended solids concentration reveal that resuspension of the hyperconcentrated layers occurs between three and eight tides after neap tides rather than during spring tides (12 to 15 tides after neaps). During these resuspension events, dissolved oxygen levels are reduced but recover by spring tides. Peak solids concentrations and critically depressed dissolved oxygen levels are out of phase with tidal current amplitude. Thus observations close to neap and spring tides do not necessaraly capture the extremes of the envelope of water quality conditions.     

五大连池不同火山喷发沉积物的细菌群落多样性研究

【目的】揭示五大连池火山区的细菌多样性。【方法】运用Illumina Miseq高通量测序技术解析五大连池不同火山喷发沉积物中细菌的群落组成和分布规律。【结果】五大连池火山区沉积物中的细菌主要包含厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、疣微菌门(Verrucomicrobia)、酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi)、放线菌门(Actinobacteria)等23个细菌门类,其中,厚壁菌门、变形菌门丰度较高,芽孢杆菌属(Bacillus)为绝对优势菌群。另外,由于火山物质的同源性,导致各沉积物中细菌的代谢通路多与C、N、S、Fe等元素的生化循环相关,群落结构及功能具有一定程度的相似性。但由于各研究区域在沉积组分、环境因素及地质演化进程上的差异,致使芽孢杆菌属、地杆菌属(Geobacter)、酸杆菌属(Acidobacterium)、嘉利翁氏菌属(Gallionella)、Blastocatella等部分种群在不同火山沉积物中呈现差异化分布,具有典型的地域适应特性。【结论】五大连池火山沉积物中含有较为丰富的细菌资源,...     

Total bacterial diversity in soil and sediment communities—A review

Advances in microbial methods have demonstrated that microorganisms globally are the dominating organisms both concerning biomass and diversity. Their functional and genetic potential may exceed that of higher organisms. Studies of bacterial diversity have been hampered by their dependence on phenotypic characterization of bacterial isolates. Molecular techniques have provided the tools for analyzing the entire bacterial community including those which we are not able to grow in the laboratory. Reassociation analysis of DNA isolated directly from the bacteria in pristine soil and marine sediment samples revealed that such environments contained in the order of 10 000 bacterial types. The diversity of the total bacterial community was approximately 170 times higher than the diversity of the collection of bacterial isolates from the same soil. The culturing conditions therefore select for a small and probably skewed fraction of the organisms present in the environment. Environmental stress and agricultural management reduce the bacterial diversity. With the reassociation technique it was demonstrated that in heavily polluted fish farm sediments the diversity was reduced by a factor of 200 as compared to pristine sediments. Here we discuss some molecular mechanisms and environmental factors controlling the bacterial diversity in soil and sediments.     

Assessment of possible sediment toxicity of contaminated sediments in Port Jackson, Sydney, Australia

A considerable amount of chemical data is available for surficial sediments in Port Jackson. Some of the highest concentrations of heavy metals, organochlorines and polycyclic aromatic hydrocarbons of any capital port occur in sediments mantling shallow tributaries and embayments close to central Sydney. However, these data have limited ability to predict adverse effects on living resources and in the absence of toxicological data, sediment quality guidelines (SQG) have been used to assess the possible adverse biological effects of sedimentary contaminants in this estuary. Several SQGs are currently available for both fresh and marine environments, but the scheme used in the current study is based on empirical analysis of matching chemical and biological data compiled by the National Oceanographic and Atmospheric Administration (NOAA) in the U.S. The NOAA SQG can be used to assess individual chemicals, or to estimate the probability of acute sediment toxicity by calculating `mean quotients' for a large range of contaminants. Although many individual chemicals in sediment exceed SQG over extensive parts of Port Jackson, `mean quotient' results suggest that only a small proportion (1%) of the harbour may be highly toxic (74% probability of toxicity). However, sediment in a considerably larger proportion of the port (almost 25%) is estimated to have a 49% probability of being toxic using the `mean quotient' approach. These results are indicative at best and contemporaneous chemical/biological/ecotoxicological studies are needed to verify the applicability of SQG developed in the U.S. for use outside North America and site specific studies of this type are still required to determine the toxicity of sediments in Port Jackson.     

Microbial communities colonising nutrient-enriched marine sediment

Sediment cores were set up to study microbial colonisation and interactions on marine sand grains under enrichment conditions. Cores were enriched with photosynthetic media in the light and dark (PL, PD) and heterotrophic media in the light and dark (HL, HD), and were incubated for 25 days. Sediment chlorophylls were then measured by acetone extraction, viable heterotrophic bacteria by plate counts, and numbers of cells mm^–2 sand grain surface by s.e.m. Chlorophyll a occurred in all sediments but was highest in the PL sediment. Bacteriochlorophyll a was only observed in the HL sediment. Heterotrophic viable counts were high in the HL and HD sediments. Dense growth of diatoms and blue-green algae, and a marine fungal Thraustochytrid sp. occurred on PL grains. The blue-green alga Schizothrix was often associated with the diatom Amphora on PL grains. Many different bacteria grew on HL and HD grains and some unusual colony and cell morphologies were recorded (Caulobacter, Flexibacter, polymer strands). Characteristic flakey material sometimes occurred in hollows on grains. The results are discussed in relation to microbial communities in low energy sedimentary environments.     

Culture-independent study of bacterial communities in tropical river sediment

Ubiquitous microbial communities in river sediments actively govern organic matter decomposition, nutrient recycling, and remediation of toxic compounds. In this study, prokaryotic diversity in two major rivers in central Thailand, the Chao Phraya (CP) and the Tha Chin (TC) distributary was investigated. Significant differences in sediment physicochemical properties, particularly silt content, were noted between the two rivers. Tagged 16S rRNA sequencing on a 454 platform showed that the sediment microbiomes were dominated by Gammaproteobacteria and sulfur/sulfate reducing Deltaproteobacteria, represented by orders Desulfobacteriales and Desulfluromonadales together with organic degraders Betaproteobacteria (orders Burkholderiales and Rhodocyclales) together with the co-existence of Bacteroidetes predominated by Sphingobacteriales. Enrichment of specific bacterial orders was found in the clayey CP and silt-rich TC sediments, including various genera with known metabolic capability on decomposition of organic matter and xenobiotic compounds. The data represent one of the pioneered works revealing heterogeneity of bacteria in river sediments in the tropics.     

夏秋季瓯江口海域鱼类数量的时空分布

本文利用2007年6月和9月瓯江口海域渔业资源调查资料,研究瓯江口鱼类密度的时空分布,分析优势种、地形地貌、海流和水文等因素对鱼类分布的影响。结果表明,6月和9月鱼类重量密度分别为150．54kg／km^2和271．53kg／km^2,尾数密度为29．11&#215;10^3ind．／km^2和14．99&#215;10^3ind．／km^2。以此推算出：6月鱼类资源量为67923kg,9月为122193kg。鱼类资源量在3个月中增长近一倍。6月的白姑鱼（Argyrosomus argentatus）和9月的龙头鱼（Harpodon nehereus）分别是本海域最重要的优势种。鱼类重量密度与尾数密度分布趋势一致,呈调查水域东部高于西部的分布趋势。6月至9月是幼鱼索饵肥育季节,索饵群体往往停留在瓯江口洞头群岛外侧宽阔海域。水深和鱼类密度相关性显著。台湾暖流、浙江沿岸水和瓯江径流的交汇是形成鱼类高密度区域重要的水文因素,表层水温是影响鱼类数量变化的重要环境因子。瓯江口鱼类数量的变化动力来自主要优势种对鱼类数量变化的回归贡献[动物学报54（6）：981—987,2008]。     

黄河口潮间带沉积物细菌群落结构特征

选取黄河口潮间带有植被覆盖和无植被覆盖两个区域采集柱状沉积物,利用实时荧光定量PCR技术和高通量测序技术分析有无植被覆盖沉积物中的细菌群落特征和功能差异,探究影响潮间带细菌群落结构的主要环境因子。结果显示,细菌丰度在有植被区域大于无植被区域。沉积物中细菌群落丰富度和多样性在有植被区域随深度的增加而增加,而在无植被区域其最高值出现在沉积物中层（14-16 cm）。两个区域在门分类水平上以变形菌（Proteobacteria）、绿弯菌（Chloroflexi）、放线菌（Actinobacteria）和酸杆菌（Acidobacteria）为主;属分类水平上的优势类群为芽孢杆菌（Bacillus）、苍白杆菌（Ochrobactrum）、拟无枝菌酸菌（Amycolatopsis）和鞘脂单胞菌（Sphingomonas）等。相关性分析发现盐度和亚硝酸盐浓度对细菌群落多样性和丰富度影响显著。功能预测分析表明,有植被区域沉积物细菌在氨基酸代谢、膜运输和碳水化合物代谢方面功能活跃,而无植被区域细菌则在核酸复制和修复、能量代谢过程方面更为活跃。     

A cohesive sediment balance for the Scheldt estuary

This article present a method to generate a cohesive sediment balance for the Scheldt estuary (The Netherlands and Belgium). In this balance the net transports have been determined on a regional scale. The complicated circulation patterns on a smaller scale are considered as a black box. The cohesive sediments in the balance are defined as the inorganic sediment with a particle size smaller than 63 μm. In the balance a distinction is made between the relatively ‘clean’ marine mud fraction and the more polluted fluvial fraction. The calculations are made on a basis of field data. The field data of the morphological changes in the estuary are based on the period of 1975–1985. The net natural transport of fluvial mud is estimated to reach beyond the mouth of the estuary. The net marine import of mud is estimated to reach beyond the brackish part of the estuary, located in Belgium. The sediment balance also provides the time scale for the response of an estuary. The time scale related to the reduction in pollution proves to be quite large. Calculations with a simple analytic model with typical values for the Scheldt estuary indicate that several decades will pass until a significant improvement in bottom sediment quality is reached even after a 100% reduction of the loading of pollutants. The presented balance is not the final answer. Improvements can be achieved by more accurate field data, smaller morphological units and verification by other methods (cf. tracer methods, mathematical models).     

Numerical modelling of suspended sediment transport in tidal estuaries: A comparison between the Tagus (Portugal) and the Scheldt (Belgium-the Netherlands)

A numerical model to simulate the transport of suspended sediment in tidal estuaries is presented. The model is applied to the two large European estuaries the Tagus (Portugal) and the Scheldt (Belgium-The Netherlands). Calculated suspended sediment concentrations compare favourably with observations in the Tagus (r=0.84) and in the Scheldt (r=0.73). The parametrization scheme indicates that the bottom content of fine sediment is correlated with depth in the Tagus; but a different relationship is used in the Scheldt. Because of tidal range differences, average suspended sediment concentrations are lower in the Tagus (80 mg l⁻¹) than in the Scheldt (130 mg l⁻¹), but a larger relative variation between spring and neap tide concentrations may occur in the Tagus.     

Bacterial communities in water and sediment shaped by paper mill pollution and indicated bacterial taxa in sediment in Daling River

Effluents from paper mills are highly toxic and are a major source of aquatic pollution. In this study, we collected water and sediment samples to examine the microbial communities using denaturing gradient gel electrophoresis and identified bacterial taxa greatly affected by paper mill pollution using next-generation sequencing data. Our results indicated that bacterial communities in downstream sediments were similar to those in paper mill discharge sites, indicating obvious effects of pollution, while bacterial communities in downstream water samples showed similar profiles to those in upstream sites, both being quite different from the bacterial communities in paper mill discharge sites. This was possibly because of the short contact period. In addition, bacterial communities in the estuary were quite different from those in other water and sediment samples, which was owing to the special habitat type. Considering the storage of paper mill pollutants in sediment and the significant effect on shifts in bacterial communities, we selected Clostridia and Epsilonproteobacteria at the class level and Fusibacter and Desulfobulbus at the genus level as bacterial indicators of paper mill pollution. To monitor the remediation of polluted aquatic environments, we propose Sphingobacteria, Alphaproteobacteria, Actinobacteria, Subdivision3, Planctomycetacia and Verrucomicrobiae at the class level and Bacillus, Steroidobacter, Nocardioides, Terrimonas, Pirellula and Methylibium at the genus level.