Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE

The bacterial candidate division JS1 dominates a number of 16S rRNA gene libraries from deep subseafloor sediments, yet its distribution in shallow, subsurface sediments has still to be fully documented. Sediment cores (down to 5.5 m) from Wadden Sea tidal flats (Neuharlingersieler Nacken and Gr?ninger Plate) were screened for JS1 16S rRNA genes using targeted PCR-denaturing gradient gel electrophoresis (DGGE), which also detects some other important Bacteria. Bacterial subpopulations at both sites were dominated by Gammaproteobacteria in the upper sediment layers (down to 2 m) and in deeper layers by members of the Chloroflexi. The deeper layers of Neuharlingersieler Nacken consisted of grey mud with low sulphate (0.1-10 mM), elevated total organic carbon (TOC) ( approximately 1-2%) and JS1 sequences were abundant. In contrast, the deeper sandy layers of Gr?ninger Plate, despite also having reduced sulphate concentrations, had lower TOC (<0.6%) with few detectable JS1 sequences. Results indicated that JS1 prefers muddy, shallow, subsurface sediments with reduced sulphate, whereas Chloroflexi may out-compete JS1 in shallow, sandy, subsurface sediments. Bacterial population changes at both sites ( approximately 2 m) were confirmed by cluster analysis of DGGE profiles, which correlated with increased recalcitrance of the organic matter. This study extends the biogeographical range of JS1. The presence of JS1 and Chloroflexi in Wadden Sea sediments demonstrates that subsurface tidal flats contain similar prokaryotic populations to those found in the deeper subseafloor biosphere.     

Niche separation of ammonia-oxidizing bacteria across a tidal freshwater marsh

Like many functional groups or guilds of microorganisms, the group of ammonia-oxidizing bacteria (AOB) consists of a number of physiologically different species or lineages. These physiological differences suggest niche differentiation among these bacteria depending on the environmental conditions. Species of AOB might be adapted to different zones in the flooding gradient of a tidal marsh. This issue has been studied by sampling sediments from different sites and depths within a tidal freshwater marsh along the river Scheldt near the village of Appels in Belgium. Samples were taken in February, April, July and October 1998. Communities of AOB in the sediment were analysed on the basis of the 16S rRNA gene by application of polymerase chain reaction in combination with denaturing gradient gel electrophoresis (DGGE). In addition, moisture content and concentrations of ammonium and nitrate were determined as well as the potential ammonia-oxidizing activities. Six different DGGE bands belonging to the beta-subclass of the Proteobacteria were observed across the marsh. The community composition of AOB was determined by the elevation in the flooding gradient as well as by the sampling depth. The presence of plants was less important for the community composition of AOB. DGGE bands affiliated with the Nitrosospira lineage were mostly found in the upper part of the marsh and in the deeper layers of the sediment. Two of the three DGGE bands related to the Nitrosomonas oligotropha lineage were more broadly distributed over the marsh, but were predominantly found in the upper layers of the sediment. Members of the environmental Nitrosomonas lineage 5 were predominantly detected in the deeper layers in the lower parts of the marsh. Potential driving factors for niche differentiation are discussed.     

Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers,denitrifiers, and anammox bacteria in sediments of estuarine tidal flats

The spatial and temporal patterns of diversity, community structure, and their drivers are fundamental issues in microbial ecology. This study aimed to investigate the relative importance of spatial and seasonal controls on the distribution of nitrogen cycling microbes in sediments of estuarine tidal flats, and to test the hypothesis that metals impact the distribution of nitrogen-cycling microbes in the coastal system. Two layers of sediment samples were collected from three estuarine tidal flats of Laizhou Bay in 2010 winter and 2011 summer. The alpha diversities (Shannon and Simpson indices) and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA), denitrifier and anammox bacteria (AMB) were revealed using denaturing gradient gel electrophoresis and clone library analysis of amoA, nosZ and 16S rRNA gene markers. We found that both AOB and AMB exhibited distinct seasonal patterns in either alpha diversity or community turnover; AOA had different alpha diversities in two layers, but neither spatial nor seasonal patterns were found for their community turnover. However, no distinct spatiotemporal pattern was observed for either diversity or community composition of nosZ-type denitrifiers. For correlations between alpha diversities and environmental factors, significant correlations were found between AOB and ammonium, temperature and As, between denitrifiers and nitrite, salinity and Pb, and between AMB and Pb, ratio of organic carbon to nitrogen, ammonium, pH and dissolved oxygen. Salinity and sediment grain size were the most important factors shaping AOB and AOA communities, respectively; whereas AMB community structure was mostly determined by temperature, dissolved oxygen, pH and heavy metals As and Cd. These results stress that ammonia oxidizers, denitrifiers and anammox bacteria have generally different distributional patterns across time and space, and heavy metals might have contributed to their differentiated distributions in coastal sediments.     

Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (∼13°N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) approximately 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.     

Effects of the burrowing mud shrimp,Upogebia yokoyai,on carbon flow and microbial activity on a tidal flat

Mud shrimps, Upogebia spp., are major constituents of macrobenthic communities in tidal flats in Japan. The impact of Upogebia yokoyai on carbon flow on tidal flats was examined by comparing CO₂ emission rates from plots with and without burrows in the Kurose River estuary, Japan. In situ CO₂ emission rates from plots with burrows were significantly higher than from those without. Laboratory measurements using sediment core samples that excluded respiration of macrobenthic organisms showed similar trends. Although there were no significant differences in grain size distribution, water content, or ignition loss between the sediment cores with and without burrows, oxidation–reduction potential was significantly higher in sediment cores with burrows. Analysis of phospholipid fatty acids (PLFA) indicated that microbial biomass and community structure did not differ significantly between cores with and without burrows. However, microbial respiration activity, as indicated by CO₂ emission rates per total PLFA content, was significantly higher in sediment cores with burrows than in those without. Our results indicate that burrows of U. yokoyai change the physicochemical conditions and increase microbial activity in the sediment, significantly affecting carbon flow in the tidal flat.     

Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns

Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67–72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.     

Bacterial diversity in sediments of the eutrophic Guanting Reservoir,China, estimated by analyses of 16S rDNA sequence

The bacterial diversity in different layers of sediment of the eutrophic Guanting Reservoir (China) was investigated using molecular ecological techniques. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA showed presence of different bacterial communities across depths of sediments. The trend was consistent with sedimentological layers as characterized by physical and chemical parameters. Sediments were sampled at the 4–6, 34–36, and 69–72 cm depths to represent upper, middle and lower layers and used to construct three 16S rDNA clone libraries. Out of a total of 760 positive clones obtained from the three sediment layers, 148 rDNA types were identified by amplified 16S rDNA restriction analysis (ARDRA) and grouped into 42 clusters or single lineages at the similarity of 70%. We used 16S rDNA sequencing to classify 60 clones representing different ARDRA clusters into nine phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia. The diversity and distribution of rDNA types across depths were much different from the chemical profile of the sediment and pollution history of the reservoir.     

青藏高原淡水湖普莫雍错和盐水湖阿翁错湖底沉积物中细菌群落的垂直分布

【目的】湖泊沉积物中存储着大量独特的微生物,这些微生物在湖泊生态系统生物地球化学循环中扮演着非常重要的角色。然而,很少有研究报道微生物群落在湖泊沉积物中的垂直分布。本文比较研究青藏高原淡水湖普莫雍错和盐水湖阿翁错沉积物在不同深度下细菌的丰度和群落结构。【方法】利用定量PCR(q PCR)和变性梯度凝胶电泳(DGGE)技术分别测定细菌群落的丰度与群落结构。【结果】定量PCR结果显示,湖泊沉积物中细菌丰度均随深度增加而降低,盐水湖阿翁错和淡水湖普莫雍错的细菌丰度分别从1011数量级降到108数量级,从1012数量级降到1010数量级。在相对应的沉积物层,淡水湖沉积物的细菌丰度比盐水湖高1-2个数量级。变性梯度凝胶电泳(DGGE)指纹图谱的分析表明,淡水湖沉积物细菌群落的DGGE条带数(丰富度)显著高于盐水湖(P=0.014);淡水与盐水湖泊沉积物细菌群落结构明显不同,同时在同一湖泊沉积物中上层(0-6 cm)和下层(7-20 cm)细菌群落结构也呈明显分异。系统发育分析表明,盐水湖阿翁错沉积物特有菌门为Gamma-变形菌、拟杆菌门、蓝细菌和栖热菌门,而淡水湖普莫雍错沉积物中特有菌门为Delta-和Beta-变形菌、酸杆菌和绿弯菌门。【结论】青藏高原淡水与盐水湖泊沉积物细菌丰度与群落结构具有明显的差异;同时,细菌群落结构在沉积物的不同深度也表现出差异。这些结果可为进一步阐明青藏高原湖泊生态系统中微生物对气候环境变化的响应提供科学依据。     

Novel uncultured Chloroflexi dechlorinate perchloroethene to trans-dichloroethene in tidal flat sediments

The marine environment represents a rich source of bio- and geogenically produced organohalogens, including the common pollutant perchloroethene (PCE). However, diversity and function of marine chloroethene-dechlorinating microorganisms are largely unknown. Here, we have studied the activity and composition of a tidal flat sediment bacterial and archaeal community from the North Sea exposed to low concentrations of PCE. After 2 weeks of incubation, PCE was rapidly dechlorinated via trichloroethene to dichloroethene (DCE). Unexpectedly, these microcosms produced 3.5-fold more trans-DCE than cis-DCE. The actively dechlorinating microbial populations were traced by stable isotope probing of rRNA with (13)C-labelled acetate for 4 days. Terminal restriction fragment length polymorphism fingerprinting and clone libraries of isotopically enriched, 'heavy'(13)C-labelled bacterial 16S rRNA revealed the populations potentially involved in reductive dechlorination. Major clone groups belonged to the Proteobacteria (50.0%; 22.4% delta-, 12.1% gamma-, 6.9% alpha-, 6.9% beta- and 1.7% epsilon-subgroup) and Chloroflexi (29.3%). Populations represented by the two dominant terminal restriction fragments were affiliated with the Dehalococcoidetes (subphylum II of the Chloroflexi), and were exclusively detected in the heavy fraction of the PCE-dechlorinating incubation. The phylogenetically novel, larger population, designated Tidal Flat Chloroflexi Cluster, was closely related to the recently discovered PCE-dechlorinating Lahn Cluster bacteria from anoxic river sediment but more distantly related to canonical Dehalococcoides spp. (92-94% sequence identity). The second population was closely related to 'Dehalobium chlorocoercia DF-1'. Both populations appear to be responsible for reductive dechlorination of highly chlorinated ethenes to predominantly trans-DCE in tidal flat sediment incubations.     

Effects of Three Polycyclic Aromatic Hydrocarbons on Sediment Bacterial Community

Mangrove sediment is susceptible to anthropogenic pollutants, including polycyclic aromatic hydrocarbons (PAHs). However, the effects of PAHs on the bacterial diversity in mangrove sediment have been rarely studied. In the present study, the effects of three types of PAHs (Naphthalene, Fluorene, and Pyrene) at three doses on sediment microbial populations were investigated by using denaturing gradient gel electrophoresis (DGGE). After 7 and 24 days of incubation of the three types of PAHs, markedly different patterns were observed in the bacterial communities. Overall, the diversity of bacterial community was suppressed before 7 days but was promoted after 24 days. Multidimensional scaling analysis suggested that the composition of bacterial communities after 7 days was distinctly distant from that after 24 days. Also despite a slight shift of bacterial abundance, the bacterial communities were relatively steady in these sediments after exposure to PAHs. In addition, DGGE suggested that the applications of three PAHs (especially PYR) had considerable effects on bacterial communities. For phylogenetic analysis, bacteria species belonging to Proteobacteria (α-, β-, and γ-), Actinobacteria, Chloroflexi, Bacteroidetes, and Planctomycetes were changed dramatically after treatment with PAHs. These results suggest that PAHs play key roles in the change of bacterial community, which may be important for understanding the relationship between PAHs and sediment microbial ecology.     

Polycyclic Aromatic Hydrocarbon-Induced Structural Shift of Bacterial Communities in Mangrove Sediment

Mangrove sediment is well known for its susceptibility to anthropogenic pollution, including polycyclic aromatic hydrocarbons (PAHs), but knowledge of the sediment microbial community structure with regards to exposure to PAHs is limited. The study aims to assess the effects of PAHs on the bacterial community of mangrove sediment using both 16s rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and traditional enrichment methods. Both the exposure time and the PAH concentration reduced the microbial diversity, as determined by the DGGE bands. Although PAHs could act as carbon sources for microorganisms, PAHs, at a concentration as low as 20 mg l⁻¹, posed a toxic effect to the microbial community. Sequencing of DGGE bands showed that marine bacteria from the genera of Vibrio, Roseobacter, and Ferrimonas were most abundant after PAH exposure, which suggests that both marine and terrestrial bacteria coexisted in the mangrove sediment, but that the marine microbes were more difficult to isolate using the traditional culture method. DGGE determination further demonstrated that the consistency among triplicates of the enriched consortia was significantly less than that of the sediment slurries. The present study reveals that the mangrove sediment microbial structure is susceptible to PAH contamination, and complex microbial community interactions occur in mangrove sediment.     

Major Changes in the Ecology of the Wadden Sea: Human Impacts, Ecosystem Engineering and Sediment Dynamics

Shallow soft-sediment systems are mostly dominated by species that, by strongly affecting sediment dynamics, modify their local environment. Such ecosystem engineering species can have either sediment-stabilizing or sediment-destabilizing effects on tidal flats. They interplay with abiotic forcing conditions (wind, tide, nutrient inputs) in driving the community structure and generating spatial heterogeneity, determining the composition of different communities of associated species, and thereby affecting the channelling of energy through different compartments in the food web. This suggests that, depending on local species composition, tidal flats may have conspicuously different geomorphology and biological functions under similar external conditions. Here we use a historical reconstruction of benthic production in the Wadden Sea to construct a framework for the relationships between human impacts, ecosystem engineering and sediment dynamics. We propose that increased sediment disturbances by human exploitation interfere with biological controls of sediment dynamics, and thereby have shifted the dominant compartments of both primary and secondary production in the Wadden Sea, transforming the intertidal from an internally regulated and spatially heterogeneous, to an externally regulated and spatially homogenous system. This framework contributes to the general understanding of the interaction between biological and environmental control of ecosystem functioning, and suggests a general framework for predicting effects of human impacts on soft-bottom ecosystems.     

Characterization of Humus Microbial Communities in Adjacent Forest Types That Differ in Nitrogen Availability

To address the link between soil microbial community composition and soil processes, we investigated the microbial communities in forest floors of two forest types that differ substantially in nitrogen availability. Cedar-hemlock (CH) and hemlock-amabilis fir (HA) forests are both common on northern Vancouver Island, B.C., occurring adjacently across the landscape. CH forest floors have low nitrogen availability and HA high nitrogen availability. Total microbial biomass was assessed using chloroform fumigation-extraction and community composition was assessed using several cultivation-independent approaches: denaturing gradient gel electrophoresis (DGGE) of the bacterial communities, ribosomal intergenic spacer analysis (RISA) of the bacterial and fungal communities, and phospholipid fatty acid (PLFA) profiles of the whole microbial community. We did not detect differences in the bacterial communities of each forest type using DGGE and RISA, but differences in the fungal communities were detected using RISA. PLFA analysis detected subtle differences in overall composition of the microbial community between the forest types, as well as in particular groups of organisms. Fungal PLFAs were more abundant in the nitrogen-poor CH forests. Bacteria were proportionally more abundant in HA forests than CH in the lower humus layer, and Gram-positive bacteria were proportionally more abundant in HA forests irrespective of layer. Bacterial and fungal communities were distinct in the F, upper humus, and lower humus layers of the forest floor and total biomass decreased in deeper layers. These results indicate that there are distinct patterns in forest floor microbial community composition at the landscape scale, which may be important for understanding nutrient availability to forest vegetation.     

Application of Molecular Techniques to the Elucidation of the Microbial Community Structure of Antique Paintings

This paper uses molecular techniques to describe the microstructure and microbiological communities of sixteenth century artwork and their relationships. The microbiological populations, analysed by denaturing gradient gel electrophoresis (DGGE), were highly influenced by the chemical composition of the pictorial layers detected by energy-dispersive X-ray analysis. DGGE revealed that the diversity of microbial communities was lower in pictorial layers composed of pigments with metals, such as Pb, Cu and Hg, than in those found in pictorial layers without such compounds. The number of cultivable microorganisms, mainly fungi and bacteria, was very low in comparison to those found by DGGE, revealing the presence of both cultivable and as-yet-uncultivated (or not viable) species in the samples analysed. Both fungi and bacteria were present in a non-random spatial distribution. Environmental scanning electron microscopy and fluorescent in situ hybridisation analyses revealed that bacterial populations were usually found in close contact with the surface of the pictorial layers, and fungal populations were located on the bacterial biofilm. This work shows, for the first time, the correlation between the diversity of the microbial populations and the chemical composition of the pictorial layers of an artwork.     

Variation in numbers and behaviour of waders during the tidal cycle: implications for the use of estuarine sediment flats

Estuarine sediment flats are essential feeding areas for waders, but their exploitation is constrained by the movements of tides. In this cyclic environment the exposure period of sediment flats decreases several fold from upper to lower flats, and the moving tidal waterline briefly creates particular conditions for waders and their prey. This study attempts to determine how the exposure period and the movement of the tide line influence the use of space and food resources by waders across the sediment flats. Wader counts and observations of feeding behaviour were carried out in all phases of the tidal cycle, in plots forming a transect from upper to lower flats, thus representing a gradient of exposure periods. Pecking, prey intake, and success rates varied little along the gradient. Some species actively followed the tide line while foraging, whereas others are evenly spread over the exposed flats. Black-tailed Godwit, Dunlin and Avocet were 'tide followers', whereas Grey Plover, Redshank and Bar-tailed Godwit were 'non-followers'. Densities of 'followers' near the tide line were up to five times higher than elsewhere. Species differed markedly in the way they used space on the flats, but in general the rate of biomass acquisition (in grams of ash-free dry weight per time exposed) was much higher in lower flats. However, this preference was insufficient to counter the much longer exposure of the upper flats, so the total amount of biomass consumed on the latter was greater. Therefore, it was in these upper flats that waders fulfilled most of their energetic needs. Consequently, upper flats are of particular importance for the conservation of wader assemblages, but because they are usually closer to shore they tend to suffer the highest pressure from disturbance and land reclamation.     

Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rDNA-based analysis, and related to physicochemical gradients

The vertical and temporal changes in microbial communities were investigated throughout the water column and sediment of the saline meromictic Lake Kaiike by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Marked depth-related changes in microbial communities were observed at the chemocline and the sediment-water interface. However, no major temporal changes in the microbial community below the chemocline were observed during the sampling period, suggesting that the ecosystem in the anoxic zone of Lake Kaiike was nearly stable. Although the sequence of the most conspicuous DGGE band throughout the anoxic water and in the top of the microbial mat was most similar to that of an anoxic, photosynthetic, green sulphur bacterium, Pelodyction luteolum DSM273 (97% similarity), it represented a new phylotype. A comparison of DGGE banding patterns of the water column and sediment samples demonstrated that specific bacteria accumulated on the bottom from the anoxic water layers, and that indigenous microbial populations were present in the sediment. The measurements of bicarbonate assimilation rates showed significant phototrophic assimilation in the chemocline and lithoautotrophic assimilation throughout the anoxic water, but were not clearly linked with net sulphide turnover rates, indicating that sulphur and carbon metabolisms were not directly correlated.     

Microbial diversity and stratification of South Pacific abyssal marine sediments

Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences.     

An actualistic perspective into Archean worlds - (cyano-)bacterially induced sedimentary structures in the siliciclastic Nhlazatse Section, 2.9 Ga Pongola Supergroup, South Africa

Extensive microbial mats colonize sandy tidal flats that form along the coasts of today's Earth. The microbenthos (mainly cyanobacteria) respond to the prevailing physical sediment dynamics by biostabilization, baffling and trapping, as well as binding. This biotic-physical interaction gives rise to characteristic microbially induced sedimentary structures (MISS) that differ greatly from both purely physical structures and from stromatolites. Actualistic studies of the MISS on modern tidal flats have been shown to be the key for understanding equivalent fossil structures that occur in tidal and shelf sandstones of all Earth ages. However, until now the fossil record of Archean MISS has been poor, and relatively few specimens have been found. This paper describes a study location that displays a unique assemblage with a multitude of exceptionally preserved MISS in the 2.9-Ga-old Pongola Supergroup, South Africa. The 'Nhlazatse Section' includes structures such as 'erosional remnants and pockets', 'multidirected ripple marks', 'polygonal oscillation cracks', and 'gas domes'. Optical and geochemical analyses support the biogenicity of microscopic textures such as filamentous laminae or 'orientated grains'. Textures resembling filaments are lined by iron oxide and hydroxides, as well as clay minerals. They contain organic matter, whose isotope composition is consistent with carbon of biological origin. The ancient tidal flats of the Nhlazatse Section record four microbial mat facies that occur in modern tidal settings as well. We distinguish endobenthic and epibenthic microbial mats, including planar, tufted, and spongy subtypes. Each microbial mat facies is characterized by a distinct set of MISS, and relates to a typical tidal zone. The microbial mat structures are preserved in situ, and are consistent with similar features constructed today by benthic cyanobacteria. However, other mat-constructing microorganisms also could have formed the structures in the Archean tidal flats.     

海南东寨港红树林不同植被土壤微生物群落结构比较

【目的】比较不同植被下红树林土壤细菌和古菌的多样性及群落结构,认识红树林土壤微生物资源多样性。【方法】直接提取红树林土壤总DNA,采用细菌通用引物27F/1492R和古菌通用引物Arch21F/Arch958R进行PCR扩增,构建细菌和古菌16S rRNA基因文库,对海南东寨港自然保护区秋茄林、无瓣海桑林和无红树林裸滩土壤的细菌和古菌多样性和群落结构进行分析和比较。【结果】3种土壤样品的细菌类群包括变形细菌门(Proteobacteria)等16个类群,其中变形细菌门(Proteobacteria)与绿屈挠菌门(Chloroflexi)是优势类群;古菌包括6个嗜泉古菌界(Crenarchaeota)类群和7个广域古菌界(Euryarchaeota)类群,分别以Marine Benthic Group C、Marine Benthic Group D为优势类群。多样性指数(H’)和物种丰富度指数(Schao1)表明,本地种秋茄林下土壤细菌和古菌的多样性指数最高,外来种无瓣海桑显著低于秋茄林,甚至明显低于相邻无红树林裸滩沉积物;不同植被下土壤细菌和古菌群落结构存在显著差异,秋茄林土壤微生物群落结构和无红树林裸滩沉积物更相似。【结论】红树林土壤微生物类群丰富,不同植被下土壤细菌和古菌多样性和群落结构存在显著差异。     

Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel)

The microbial community structure of an anoxic profundal lake sediment, i.e., subtropical Lake Kinneret, was analysed with respect to its composition by culture-independent molecular methods including terminal restriction fragment length polymorphism (T-RFLP) analysis, comparative sequence analysis, and quantitative real-time PCR. In particular we were interested in the structure, species composition, and relative abundance of the overall microbial community in the methanogenic sediment layer (0-10 cm depth). Pairwise comparison of archaeal and bacterial 16S rRNA gene T-RFLP profiles obtained from three independent samplings indicated stability of the microbial community. The numbers of Archaea and Bacteria, quantified by real-time PCR, amounted to about 10(8) and 10(10) 16S rRNA gene copies cm(-3) sediment, respectively, suggesting that Archaea may account for only a minor fraction (approximately 1%) of the total prokaryotic community. Hydrogenotrophic Methanomicrobiales and acetoclastic Methanosaeta spp. dominated T-RFLP profiles of the archaeal community. T-RFLP profiles of the bacterial community were dominated by Deltaproteobacteria, sulphate reducers and syntrophs in particular. The second most abundant group was assigned to the Bacteroidetes-Chlorobi-group. Only one bacterial group, which was affiliated with halorespiring bacteria of subphylum II of the Chloroflexi, showed variation in abundance within the sediment samples investigated. Our study gives a comprehensive insight into the structure of the bacterial and archaeal community of a profundal lake sediment, indicating that sulphate reducers, syntrophs, bacteroidetes, halorespirers and methanogens are of particular importance in Lake Kinneret sediment.