东寨港红树林沉积物中微生物群落结构特征及其对环境的响应

在红树林覆盖区域和光滩沉积物中存在着丰富的微生物群落,这些微生物在驱动红树林湿地的生物地球化学过程中起着至关重要的作用.深入了解东寨港红树林湿地沉积物中微生物的多样性分布特征,对探究东寨港红树林湿地中的生物地球化学过程和湿地的生态保护具有重要意义.本研究采用Illumina Miseq高通量测序技术,在东寨港的演丰西河...     

A comparison of sediment microbial communities associated with<Emphasis Type="Italic">Phragmites australis</Emphasis> and<Emphasis Type="Italic">Spartina alterniflora</Emphasis> in two brackish wetlands of New Jersey

The extensive spread ofPhragmites australis throughout brackish marshes on the East Coast of the United States is a major factor governing management and restoration decisions because it is assumed that biogeochemical functions are altered by the invasion. Microbial activity is important in providing wetland biogeochemical functions such as carbon and nitrogen cycling, but there is little known about sediment microbial communities inPhragmites marshes. Microbial populations associated with invasivePhragmites vegetation and with native salt marsh cordgrass,Spartina alterniflora, may differ in the relative abundance of microbial taxa (community structure) and in the ability of this biota to decompose organic substrates (community biogeochemical function). This study compares sediment microbial communities associated withPhragmites andSpartina vegetation in an undisturbed brackish marsh near Tuckerton, New Jersey (MUL), and in a brackish marsh in the anthropogenically affected Hackensack meadowlands (SMC). We use phospholipid fatty acid (PLFA) analysis and enzymataic activity to profile sediment microbial communities associated with both plants in each site. Sediment analyses include bulk density, total organic matter, and root biomass. PLFA profiles indicate that the microbial communities differ between sites with the undisturbed site exhibiting greater fatty acid richness (62 PLFA recovered from MUL versus 38 from SMC). Activity of the 5 enzymes analyzed (β-glucosidase, acid phosphatase, chitobiase, and 2 oxidases) was higher in the undisturbed site. Differences between vegetation species as measured by Principal Components Analysis were significantly greater at the undisturbed MUL site than at SMC, and patterns of enzyme activity and PLFAs did not correspond to patterns of root biomass. We suggest that in natural wetland sediments, macrophyte rhizosphere effects influence the community composition of sediment microbial populations. Physical and chemical site disturbances may impose limits on these rhizosphere effects, decreasing sediment microbial diversity and potentially, microbial biogeochemical functions.     

Microbial diversity in waters,sediments and microbial mats evaluated using fatty acid-based methods

The review summarises recent advances towards a greater comprehensive assessment of microbial diversity in aquatic environments using the fatty acid methyl esters and phospholipid fatty acids approaches. These methods are commonly used in microbial ecology because they do not require the culturing of micro-organisms, are quantitative and reproducible and provide valuable information regarding the structure of entire microbial communities. Because some fatty acids are associated with taxonomic and functional groups of micro-organisms, they allow particular groups of micro-organisms to be distinguished. The integration of fatty acid-based methods with stable isotopes, RNA and DNA analyses enhances our knowledge of the role of micro-organisms in global nutrient cycles, functional activity and phylogenetic lineages within microbial communities. Additionally, the analysis of fatty acid profiles enables the shifts in the microbial diversity in pristine and contaminated environments to be monitored. The main objective of this review is to present the use of lipid-based approaches for the characterisation of microbial communities in water columns, sediments and biomats.     

太湖沉积物中微生物多样性垂向分布特征

运用化学分析方法和PCR-DGGE技术,从沉积物化学及分子生物学角度对太湖沉积物理化性质(pH、Eh)、营养盐及微生物多样性的垂向分布及相关性进行研究。结果表明:沉积物-上覆水接触界面处于轻度还原状态,在表层8.0cm左右以下,Eh随沉积深度的增加迅速下降,还原性逐渐增强,到15.0～22.5cm深度区间内,Eh值基本稳定,还原性最强,之后随深度的进一步增加,Eh呈"之"型缓慢升高。沉积物pH随深度的增加先降低后缓慢升高,pH在整个剖面上变化幅度不大,在7.2～7.6变动。沉积物中含有丰富的营养盐,总氮(TN)、总磷(TP)最高含量分数和有机质(OM)的最高百分比分别为2.436mg/g、0.731mg/g和3.817%,其剖面特征表明,沉积物表层TN和OM远高于底层,其含量随深度增加而降低。TP随着沉积深度的增加呈"之"型缓慢减少。不同深度沉积物的微生物群落呈现出明显的空间分布多样性差异,不同深度沉积物的微生物群落结构之间的相似性和动态性存在差异。多元相关分析结果显示,TN与OM显著相关,理化指标、营养盐中任一指标含量与微生物群落多样性指标之间存在相关性,但不显著,微生物多样性是营养盐及环境物理、化学和生物等多方面共同作用的结果。     

Temperature adaptation of microbial communities in different horizons of Siberian permafrost-affected soils from the Lena Delta

The cell membrane phospholipid (PL) inventory of microbial populations in a Siberian permafrost soil of the Lena Delta was analysed to examine as to how the microbial populations within different horizons of the active layer were adapted to the extreme temperature gradient in this environment. One surface-near and one permafrost-near soil sample were taken from the active layer on Samoylov Island in the southern central Lena Delta (Siberia) and in each case incubated at 4 and 28 °C. Subsequently, the phospholipid cell membrane composition of the indigenous microbial populations was qualitatively and quantitatively determined and compared. In both horizons, the incubation at 4 °C is characterized by a shift in the PL inventory to more short chain fatty acids. A significant trend in the proportions of saturated and unsaturated fatty acids, however, was not detected. A higher proportion of both short chain and unsaturated fatty acids counterbalances the effect of decreasing cell membrane fluidity with decreasing environmental temperature. Thus, the adaptation of the permafrost microbial populations within the different horizons to varying ambient temperature conditions appears to be mainly regulated by the chain length of the phospholipid fatty acids. Although there is almost no change in the proportions of unsaturated fatty acids between the 4 and 28 °C incubation experiments, the permafrost-near horizon in general contains more unsaturated fatty acids than the surface-near horizon and a higher proportion of short chain fatty acids. This suggests that the lipid inventory of the microbial population nearer to the perennially frozen ground is more adapted to lower temperatures than that of the microbial community from the surface-near horizon, which seems to show a higher flexibility toward higher temperature conditions. The permafrost-near horizon appears to be dominated by psychrophilic species, while the surface-near horizon is characterized by a mesophilic-dominated microbial community.     

Early diagenesis of fatty acids in lacustrine sediments—III. Changes in fatty acid composition in the sediments from a brackish water lake

A 3-m sediment core taken from Lake Suigetsu, in which a shift from fresh to brackish water occurred about three hundred years ago, has been examined for variation with depth of organic carbon and fatty acids. From the difference in total amounts of sulphur between sediments under fresh and brackish water environments, the surface sediments above approximately 35 cm depth were deduced to be accumulated under a brackish water environment. The total contents of organic carbon and fatty acids, and percentage composition of fatty acids gave discontinuous profiles above and below the 35–40 cm sediment layer. At a depth of 12.5 cm, the distribution in chain length of the fatty acids changed from a unimodal (the predominance of C₁₂-C₁₈ over C₂₀-C₃₄) to a bimodal pattern, which was mirrored by the composition diversity index (CDI).Although the fatty acids in the surface sediments (0–40 cm) from Lake Suigetsu seemed to suffer milder degradation through microbial activity than those in a core (0–150 cm) from Lake Suwa, a freshwater eutrophic lake, both lacustrine sediments showed similar trends in the alteration of fatty acid composition with depth.     

Distribution characteristics and factors influencing microbial communities in the core soils of a seawater intrusion area in Longkou City,China

Microbes live throughout the soil profile. Microbial communities in subsurface horizons are impacted by a saltwater–freshwater transition zone formed by seawater intrusion (SWI) in coastal regions. The main purpose of this study is to explore the changes in microbial communities within the soil profile because of SWI. The study characterizes the depth-dependent distributions of bacterial and archaeal communities through high-throughput sequencing of 16S rRNA gene amplicons by collecting surface soil and deep core samples at nine soil depths in Longkou City, China. The results showed that although microbial communities were considerably impacted by SWI in both horizontal and vertical domains, the extent of these effects was variable. The soil depth strongly influenced the microbial communities, and the microbial diversity and community structure were significantly different (p < 0.05) at various depths. Compared with SWI, soil depth was a greater influencing factor for microbial diversity and community structure. Furthermore, soil microbial community structure was closely related to the environmental conditions, among which the most significant environmental factors were soil depth, pH, organic carbon, and total nitrogen.

     

Water and sediment quality assessment in the mid-Black Sea coast of Turkey using multivariate statistical techniques

The aim of this study was to investigate the water and sediment quality in the mid-Black Sea coast of Turkey. The samples were collected from six stations during 2007. Investigated parameters were total carbon (TC), total inorganic carbon (TIC), total organic carbon (TOC), ammonium-nitrogen (NH₄-N), nitrate-nitrogen (NO₃-N), nitrite-nitrogen (NO₂-N), total phosphorus (TP), sulphate, total hardness, methylene blue active substances (MBAS), phenol, adsorbable organic halogens (AOX), dissolved oxygen (DO), pH and electrical conductivity (EC) in water samples and TC, TIC, TOC, TP, pH, electrical conductivity (EC), redox potential (Eh) and water content (WC) in sediment samples. Different multivariate statistical techniques were used to evaluate variations in surface water and sediment quality. Principal component analysis helped in identifying the factors or sources responsible for water and sediment quality variations. Five factors were found responsible for 87.63% of the total variance in the surface waters. In sediments, three factors explained 84.73% of the observed total variance. Cluster analysis classified the monitoring sites into two groups based on similarities of water and sediment quality characteristics.     

Microbial lipids from a nearshore sediment from Bowling Green Bay,North Queensland: The fatty acid composition of intact lipid fractions

Samples from a sediment core collected in Bowling Green Bay, North Queensland have been analysed for hexane/isopropanol extractable lipids and fatty acids. These data revealed a subsurface lipid abundance maximum at 3–4 cm depth and consistent low total fatty acid abundances (ca 2 μg/g) in the deeper samples ( > 10 cm depth). Lipid phosphate was below the level of detection in all the samples. Bacterial community structure was found to vary markedly in the upper 10 cm of the core, with the 18:1Δ11 bacterial chemotype predominant in the surface sediment and trans-acid chemotypes dominating in the 3–4 cm depth sediment. Based on the fatty acid composition, the bacterial biomass was estimated to vary from 199 μg/g at 3–4 cm depth toca 8 μg/g at 11–13 cm depth, although the fatty acid distributions indicated possible interference from protozoan detritus. In order to test this possibility, a surface sediment sample from a nearby site was extracted and analysed for fatty acids in lipid fractions separated by silica column chromatography. The fatty acid distributions in lipid fractions containing wax/steryl esters, triacylglycerols, glycolipids and phospholipids were markedly different. These analyses were interpreted in terms of fatty acid contributions to the extractable lipids from bacteria, cyanobacteria, protozoan detritus and highly degraded organic matter.     

Relationships between microbial communities and environmental parameters at sites impacted by mining of volcanogenic massive sulfide deposits,Prince William Sound,Alaska

The relations among geochemical parameters and sediment microbial communities were examined at three shoreline sites in the Prince William Sound, Alaska, which display varying degrees of impact by acid-rock drainage (ARD) associated with historic mining of volcanogenic massive sulfide deposits. Microbial communities were examined using total fatty acid methyl esters (FAMEs), a class of compounds derived from lipids produced by eukaryotes and prokaryotes (bacteria and Archaea); standard extraction techniques detect FAMEs from both living (viable) and dead (non-viable) biomass, but do not detect Archaeal FAMEs. Biomass and diversity (as estimated by FAMEs) varied strongly as a function of position in the tidal zone, not by study site; subtidal muds, Fe oxyhydroxide undergoing biogenic reductive dissolution, and peat-rich intertidal sediment had the highest values. These estimates were lowest in acid-generating, intertidal zone sediment; if valid, the estimates suggest that only one or two bacterial species predominate in these communities, and/or that Archeal species are important members of the microbial community in this sediment.     

城市纳污河流沉积物微生物群落结构特征

以南京市运粮河沉积物为研究对象,通过磷脂脂肪酸(PLFA)技术分析了不同水期城市纳污河流沉积物微生物群落结构特征。结果表明:在不同的水期运粮河沉积物微生物量出现了显著差异,温度是导致微生物量在丰、平、枯三期出现显著差异的主要因素(P<0.05);在相同水期,营养物质含量高的地方对应着高的微生物量;16:0 iso、17:0 anteiso、15:0 iso这几种PLFA所指示的革兰氏阳性菌(G+)是影响运粮河沉积物微生物群落构成的主要菌落,导致沉积物微生物群落结构出现显著差异的环境因素是水期;单不饱和/支链脂肪酸比值可以作为反映水环境系统整体营养水平的指标,在C/N比值升高时微生物会将单不饱和脂肪酸转变成环丙基或者饱和脂肪酸以适应新的环境;PLFA含量比[c(i15:0)+c(i17:0)]/[c(a15:0)+c(a17:0)]可以作为指示水环境碳素含量的标志。     

Spatial differences in macroinvertebrate communities in intertidal seagrass habitats and unvegetated sediment in three New Zealand estuaries

This study investigated macroinvertebrate community composition in seagrass beds at a range of spatial scales, with an emphasis on the transition between vegetated and unvegetated sediment. At four intertidal sites in three New Zealand estuaries (Whangamata, Wharekawa, and Whangapoua Harbours), a large continuous bed of seagrass (Zostera capricorni) was selected with adjacent unvegetated sediment. Macroinvertebrate community composition and biomass, as well as sediment characteristics, were determined at sampling locations 1 and 50 m inside seagrass beds, and 1, 10, and 50 m outside seagrass beds. Analysis of univariate measures of community composition (total abundance, number of species, and diversity) and total biomass indicated significant differences among sites and sampling locations, but contrary to many previous studies these measures were not higher inside than outside the seagrass beds. Multivariate analysis indicated that sites with high seagrass biomass supported a similar community composition. The remaining sampling locations were clustered by site, but there were also significant differences in community composition among sampling locations within a site. There were distinctive communities at the edge of seagrass beds at sites with high seagrass biomass, and evidence that the effects of seagrass beds may extend into the unvegetated sediment. At the low seagrass biomass site there was no evidence of any edge effects, although community composition differed inside and outside the bed. Differences in community composition were driven primarily by small changes in the relative abundance of the dominant taxa. At high seagrass biomass sites the absence of deep-burrowing polychaetes and low numbers of bivalves suggests that one possible mechanism underlying the observed variation in community composition was inhibition by the dense root-rhizome mat. The results of this study emphasize the need to consider the linkages between habitats in heterogeneous estuarine landscapes and how those linkages vary among sites, if the structure and functioning of macroinvertebrate communities in seagrass habitats are to be understood.     

南海北部九龙甲烷礁邻区沉积物层中垂向细菌群落结构特征研究

本研究应用微生物16S rRNA-DGGE和T-RFLP技术,结合环境参数,对我国天然气水合物潜在区南海九龙甲烷礁附近973-4柱状样沉积物中3个层位12个不同深度(表层20 cm至382 cm,中层552 cm至796 cm,深层862 cm至1 196 cm)细菌群落结构及其分布进行了对比研究.其中T-RFLP实验表明,细菌丰度、香农指数和均匀度变化趋势相同,由深层到716 cm处先降后升,中层716 cm深度范围处微生物群落丰度、均匀度、香农指数相对较高,716 cm至表层先降后升.DGGE图谱和T-RFLP色谱峰聚类分析表明:表层20 cm至192 cm相似性较高,表层236 cm至382 cm与深层1 082 cm、1 196 cm群落结构相似性较高,但中层沉积物中微生物群落结构与表层及深层均有较大差异.环境参数表明中层甲烷含量较高,推测甲烷是影响微生物群落结构差异的主要因素之一.T-RFLP色谱峰与微生物数据库比对及DGGE条带测序也表明了:本区变形杆菌(Proteobacteria)为优势菌群,其中α-、γ-、δ-变形杆菌(Proteobacteria)为主要的细菌亚群,其他细菌包括放线菌(Actinobacteria)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)为次优势菌群.甲烷含量较高的中层,甲烷氧化菌(Methanotrophs),硫还原菌(Sulfate-reducing bacteria)等与甲烷密切相关的细菌均有被检测到,表明该区域存在与天然气水合物的分解释放相关的微生物群落.     

The Response of Macrobenthic Communities to Environmental Variability in Tropical Coastal Waters

The relative contributions of spatial and temporal fluctuations are different in shaping natural communities in a tropical coastal/estuarine system. Understanding how coastal communities respond to these fluctuations is still equivocal, and thus, available data are rare. Here, multiple analytical approaches were used to identify key spatial and temporal factors, and to quantify their relative roles in shaping a macrobenthic community through space (contamination degree, physical parameters, and sediment characteristics) and time (climatic factors, season, and year). A dataset of eight sampling times was analyzed over a period of 2 years, in which macrobenthic species abundances were sampled. A total of 33 species were identified, including 18 bivalves, 5 gastropods, and 4 crustaceans. The other taxa were less diverse. The results show that there were no significant temporal changes of macrobenthic community structure, but spatial changes were significant and synchronized with environmental factors (i.e., sediment characteristics, water depth, and the distance from anthropogenic sources). This study demonstrates that spatial factors played a primary role in structuring of macrobenthic assemblages, whereas the influence of temporal factors appeared less across geographically distinct sites. Thus, temporal variation of a coastal macrobenthic community appears to be controlled by partly different processes at different scales.     

Suspended material in Narragansett Bay: fatty acid and hydrocarbon composition

Suspended material collected at various stations in Narragansett Bay was analyzed for fatty acids and hydrocarbons. The qualitative and quantitative distributions of these compounds indicated that the influence of sewage and other pollutants was greatest in the river areas. Based on concentrations of polyunsaturated fatty acids, the highest densities of phytoplankton were interpreted to occur at the mid and lower Bay stations, and the percentage of phytoplankton in suspended material was estimated from the concentration of heneicosahexaene. The concentrations of fatty acids and hydrocarbons in the suspended material decreased from the river stations to the mid and lower Bay stations, closely following a similar trend observed in the sediment. Possible sources of the suspended material and the influence of these sources on this material in various areas of the Bay are discussed, and attempts are made to interrelate the suspended material, resuspended sediment, phytoplankton, and sewage effluent with chemical and biochemical diagenetic changes.     

通辽科尔沁地区土壤微生物群落结构和功能及其影响因素

农业作为通辽科尔沁地区的传统产业,是当地重要经济产业之一.了解土壤微生物群落结构和功能及其影响因素对农作物种植、污染土地修复等具有重要意义.采用Illumina Miseq高通量测序技术、FAPROTAX.1.1功能预测平台等方法,在该区采集71个土壤样品,分析其地球化学特征和微生物群落特征并对微生物群落进行功能预测,同时探讨不同环境因子和空间因子对微生物群落的影响.结果显示:微生物群落由变形菌门（Proteobacteria）（19.77%）、奇古菌门（Thaumarchaeota）（17.85%）、酸杆菌门（Acidobacteria）（17.14%）和放线菌门（Actinobacteria）（15.58%）等构成;功能预测表明该区存在大量活跃的参与氮循环过程的微生物功能群,其中有氧氨氧化功能群为该区的优势微生物功能群.方差分解分析显示,在对微生物群落结构差异的可解释范围内环境因子比空间因子的解释量更大.Mantel检验结果显示,整体微生物群落与土壤pH、EC、TN、C/N及Mg、Na、Sr元素含量显著相关（p < 0.05）.综合分析表明,pH、EC和Sr元素含量是影响通辽科尔沁地区土壤微生物群落结构和功能及多样性的主要环境因素.      

Measurement of methanotroph and methanogen signature phosopholipids for use in assessment of biomass and community structure in model systems

Methanotrophic biomass and community structure were assessed for a soil column enriched with natural gas. An increase in microbial biomass, based on phospholipid ester-linked fatty acids (PLFA), was apparent for the natural gas-enriched column relative to a control column and untreated surface soil. Following GC-MS analyses of the derivatized monounsaturated fatty acids, the major component (22% of the PLFA) of the natural gas-enriched column was identified as 18·1Δ 10c. This relatively novel fatty acid has only been previously reported as a major component in methanotrophs. Its presence in the soil, together with other supportive evidence, implies that this microbial metabolic group makes a large contribution to the column flora. Other microbial groups were also recognized and differences compared between the soils analysed. A recently developed HPLC method for the separation and characterisation of archaebacterial phospholipid-derived signature di- and tetra-ether lipids was used to examine methane-producing digesters. With this technique, methanogenic biomasses of approximately 10¹¹ bacteria per g dry weight of digestor material were determined. Differences between ratios of diether to tetraether phospholipids were apparent for the digestors analysed, though the causes are at this stage unknown. Taken together, these two methods can be used to estimate methanotrophic and methanogenic contributions in both model systems and environmental samples.     

Organic geochemistry of Walvis Bay diatomaceous ooze—I. Occurrence and significance of the fatty acids

Diatomaceous ooze of the shelf off Walvis Bay (S.W. Africa) was analysed for lipid material. The lipids from the sediment consist of a mixture of hydrocarbons, alcohols, ketones, fatty acids, sterols, carotenoid pigments and chlorophylls. The total fatty acid mixture has been analysed by capillary gas chromatography mass spectrometry and shown to consist of straight chain, iso-, anteiso- and isoprenoid acids. The environmental setting of the S.W. African shelf (Walvis Bay) makes it possible to discuss these fatty acids as markers for the fate of organic matter. The acids in the sediment point to a generation during passage of algal lipids through levels of microbial activity either on or slightly above the burial surface.     

神农架大九湖不同生境表土磷脂脂肪酸揭示的微生物群落结构差异

磷脂脂肪酸(phospholipid fatty acid,PLFAs)是活体微生物细胞膜的重要组成部分,微生物通过改变细胞膜中PLFA组成,快速响应环境变化.目前,表土PLFAs研究主要集中于季节和植被群落变化对微生物群落结构影响,对于不同生境下表土PLFAs揭示的微生物群落结构的差异性尚不明确.基于此,对神农架大九湖7种不同生境表土进行PLFAs研究.结果表明,表土样品PLFAs集中分布于C₁₄到C₁₉;除湿生泥炭沼泽和湿生半退化沼泽生境外,其他生境以n16:0为主峰.不同生境的PLFAs含量差异较大,沼泽生境TPLFAs含量是草甸及阔叶林生境下的3~8倍.PLFAs组成还揭示出生境间主要受到pH和含水率的影响,微生物群落结构存在差异.不同生境下表层土壤PLFAs揭示的微生物丰度和群落结构具有一定的相似性及差异性.运用PLFAs对微生物量及微生物群落结构的划分将有助于更好的了解区域生态系统中微生物群落结构的变化,为研究微生物参与碳循环及古生态研究奠定基础.      

Effects of contamination of single and combined cadmium and mercury on the soil microbial community structural diversity and functional diversity

To assess the effects of single and combined pollution of cadmium (Cd) and mercury (Hg) on soil micro-bial community structural and functional diversities, an incubation experiment was conducted, by employing two soils, namely, the marine sediment silty loam soil and the yellowish-red soil, in which five levels of Cd, Hg and Cd and Hg in combination were added. After being incubated for 56 days, the phospholipid fatty acids (PLFAs) profile and sole carbon source utilization pattern (BIOLOG) of the samples were tested. The results showed that the compo-sition of the microbial communities changed significantly at different levels of metals application. The principal component analyses (PCA) of PLFAs indicated that the structure of the microbial community was also significantly altered with increasing levels of metals, with increasing PLFAs biomarkers for fungi and actinomycetes, and in-creasing ratio of Gram-positive to Gram-negative bacteria. Sole carbon source utilization pattern analysis revealed that single and combined application of Cd and Hg inhibited significantly the functional activity of soil microorgan-isms, the functional diversity indices [Richness (S), Shannon-Wiener indices (H) and Evenness (EH)] were signifi-cantly lower in polluted soils than those in non-polluted soils, which also significantly altered with increasing levels of metals. PCA for the sole carbon source utilization pattern also indicated that the metal contamination could result in a variable soil microbial community. The results revealed that the combination of Cd and Hg had higher toxicity to soil microbial community structural and functional diversities than the individual application of Cd or Hg.