Microbial diversity and community structure in Fynbos soil

The Fynbos biome in South Africa is renowned for its high plant diversity and the conservation of this area is particularly important for the region. This is especially true in the case of endangered vegetation types on the lowlands such as Sand Fynbos, of which only small fragments remain. The question is thus whether the diversity of the above‐ground flora is mirrored in the below‐ground microbial communities. In order to determine the relationship of the above‐ and below‐ground communities, the soil community composition of both fungal and bacterial groups in Sand Fynbos was characterized over space and time. A molecular approach was used based on the isolation of total soil genomic DNA and automated ribosomal intergenic spacer analysis of bacterial and fungal communities. Soil from four different sites was compared to resolve the microbial diversity of eubacterial and fungal groups on a local (alpha diversity) scale as well as a landscape scale (beta diversity). The community structures from different sites were compared and found to exhibit strong spatial patterns which remained stable over time. The plant community data were compared with the fungal and the bacterial communities. We concluded that the microbial communities in the Sand Fynbos are highly diverse and closely linked to the above‐ground floral communities.     

Transport and distribution of sediments along the Ligurian coast

A study of the granulometric, mineralogical and chemical composition of surface sediments and suspended particulate matter in the coastal area between Varazze and Cape Noli (Ligurian Sea), provided useful information on transport and sedimentation processes in the area. Sediments samples from the shelf were highly heterogeneous, ranging from pelites to sands. Minerals typical of individual river basins were found close to river mouths, indicating a limited sediment transport along the coast. Chemical and textural characteristics of the suspended particulate matter indicated that the longshore sediment transport is influenced by the presence of a submarine canyon; material coming from the east, following the Ligurian current, is partially diverted offshore along the canyon axis. The coastline pattern, some harbor artifacts, and the peculiar morphology of the shelf are all factors controlling the direction of sediment transport.     

Characterization of a mercury-reducing Bacillus cereus strain isolated from the Pulicat Lake sediments, south east coast of India

Pulicat Lake sediments are often severely polluted with the toxic heavy metal mercury. Several mercury-resistant strains of Bacillus species were isolated from the sediments and all the isolates exhibited broad spectrum resistance (resistance to both organic and inorganic mercuric compounds). Plasmid curing assay showed that all the isolated Bacillus strains carry chromosomally borne mercury resistance. Polymerase chain reaction and southern hybridization analyses using merA and merB3 gene primers/probes showed that five of the isolated Bacillus strains carry sequences similar to known merA and merB3 genes. Results of multiple sequence alignment revealed 99% similarity with merA and merB3 of TnMERI1 (class II transposons). Other mercury resistant Bacillus species lacking homology to these genes were not able to volatilize mercuric chloride, indicating the presence of other modes of resistance to mercuric compounds.     

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities of marine sands. Surprisingly, only 3–5% of all bacterial types of a given depth zone were present at all times, but 50–80% of them belonged to the most abundant types in the data set. About 60–70% of the bacterial types consisted of tag sequences occurring only once over a period of 1 year. Most members of the rare biosphere did not become abundant at any time or at any sediment depth, but varied significantly with environmental parameters associated with nutritional stress. Despite the large proportion and turnover of rare organisms, the overall community patterns were driven by deterministic relationships associated with seasonal fluctuations in key biogeochemical parameters related to primary productivity. The maintenance of major biogeochemical functions throughout the observation period suggests that the small proportion of resident bacterial types in sands perform the key biogeochemical processes, with minimal effects from the rare fraction of the communities.     

Potential rates and pathways of microbial nitrate reduction in coastal sediments

Nitrate reduction plays a key role in the biogeochemical dynamics and microbial ecology of coastal sediments. Potential rates of nitrate reduction were measured on undisturbed sediment slices from two eutrophic coastal environments using flow-through reactors (FTR). Maximum potential nitrate reduction rates ranged over an order of magnitude, with values of up to 933 nmol cm(-3) h(-1), whereas affinity constants for NO(3) (-) fell mostly between 200 and 600 microM. Homogenized sediment slurries systematically yielded higher rates of nitrate reduction than the FTR experiments. Dentrification was the major nitrate removal pathway in the sediments, although excess ammonium production indicated a contribution of dissimilatory nitrate reduction to ammonium under nitrate-limiting conditions.     

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.     

Liana diversity and distribution in four tropical dry evergreen forests on the Coromandel coast of south India

Liana diversity was inventoried in four tropical dry evergreen forest sites that are characterized by numerous trees, of short stature and small diameter, and a varying degree of anthropogenic disturbance, on the Coromandel coast of south India. A 1-ha plot was established in each of the four sites and was subdivided into 100 quadrats of 10 m× 10 m. All lianas 1 cm diameter at breast height (dbh) rooted within the plot were enumerated. The species richness and density of lianas, with respect to site disturbance and forest stature, varied across the sites. Liana density totaled 3307 individuals (range 497–1163 individuals ha^–1) and species richness totaled 39 species (range 24–29 species ha^–1) representing 34 genera and 24 families. Combretaceae, Asclepiadaceae, Capparaceae and Vitaceae were the well-represented families. The top five species Strychnos minor, Combretum albidum, Derris ovalifolia, Jasminum angustifolium and Reissantia indica contributed 55% of total density. The slopes of the species–area curves were different for each of the four sites and the curve stabilized in only one site. Of the four climbing modes recognized among the total 39 species, 18 were twiners (56% of the total density). Eight species (24% of density) were tendril climbers and 12 species (16% of density) were scramblers. Hugonia mystax was the only hook climber. All the 39 species and 88% of liana density were encountered within a category of 6 cm dbh or less, and a similar pattern prevailed in the individual sites. Of the three diaspore dispersal modes found among the 39 liana species, animal (64%) and wind (23%) dispersal were predominant over the autochorous mode (13%). Liana diversity and distribution in dry forest communities appear to be influenced by forest stature and site disturbance levels. In the light of the extent of liana diversity and sacred grove status of the study sites, the need for forest conservation, involving local people, is emphasized.     

Fractionation,mobility and multivariate statistical evaluation of metals in marine sediments of Cape Town Harbour,South Africa

Abstract

Distribution of possible chemical forms of Al, Si, Sn, Pb, Zn, Fe, Hg, Cd and Cu in marine sediments of Cape Town harbour was investigated using a modified Tessier’s sequential extraction procedure and ICP-MS and ICP-AES for heavy metals determination. The mean fractions for all metals at all locations were: 1.5–7196 mg kg^-1 for Si, 7.79–7266 mg kg^-1 for Al, 161-639 mg kg^-1 for Cu, 19–41978 mg kg^-1 for Fe, 2.83–5864 mg kg^-1 for Zn, 1.45–13.26 mg kg^-1for Cd, 9.87–223 mg kg^-1 for Sn, 11.98-979 mg kg^-1 for Pb and 0.13–5.93 mg kg^-1 for Hg. Si, Al and Zn were mostly associated with Fe–Mn oxides, whereas Sn and Hg were mainly bound to residual and organic matter. Pb existed mainly in the residual and iron/manganese oxide phases while Cd was evenly distributed in all the five phases. The loading plots of heavy metals bound to the various chemical forms, as well as Pearson correlation coefficients, enabled the determination binding relationship. Pb, Sn and Hg exhibited similar binding behaviour which indicated an anthropogenic point source from wastes from the ship maintenance workshop, and the presence of Sn in the organic phase can be identified with the use of anti-fouling paints at the harbour, whereas Al, Fe, Si, Cu and Zn would probably be of natural origin. Lastly Cd probably came from a diffuse pollution sources in the harbour due to its unique binding characteristic. The mobility of heavy metals varied depending on location and the heavy metal type. The mobility of metals followed the order: Si > Zn > Fe > Cu> Al> Cd> Pb > Sn > Hg. The high percentage of Cd and Pb in the bioavailable forms suggested the need to keep close surveillance on these metals because of their high toxicity.     

Microbial metabolism in surface sediments and its role in the immobilization of phosphorus in oligotrophic lake sediments

Rapid microbial metabolism and a large phosphorus uptake potential were observed in surface sediments of Lake George, New York. This sediment (termed the flocculent layer) also exhibited a phosphorus limited condition and a large reservoir of inorganic phosphorus associated with humic substances. These observations suggest that the empirically observed phosphorus retention in oligotrophic lake sediments may be promoted by a rapid cycling of phosphorus between microflora and its associated organic matter.     

扎龙湿地不同生境的昆虫多样性

为了探讨湿地不同生境对昆虫物种多样性的影响,对扎龙湿地8种生境的昆虫进行了系统调查.共捕获昆虫5822只,分属11目58科143种,其中直翅目、双翅目、蜻蜒目为扎龙湿地的优势类群.不同生境中,草原草甸昆虫多样性最高,湖边生境多样性指数和均匀度指数均较高,杂草甸均最低.聚类分析和主分量分析结果表明,不同生境的昆虫群落相似性与水资源状况和植被类型有关,捕食性类群种类数和个体数量对昆虫群落稳定性具有重要的调控作用.湖边生境昆虫群落稳定性最强,湿草甸稳定性最弱.湿地水资源状况能影响昆虫生存生境,进而影响昆虫群落的组成和分布格局.     

黄海山东海域春、秋季鱼类群落多样性

根据2006年春季(5月)和秋季(10月)黄海山东海域疏目变水层双拖网调查数据,作者对该海域鱼类群落多样性、空间分布及长度谱特征进行了研究。调查共捕获鱼类61种,其中鲈形目种类最多(27种),其次为鲱形目(8种)和鲉形目(7种);按摄食类型可分为浮游动物食性、浮游动物/底栖动物食性、底栖动物食性、底栖动物/游泳动物食性、游泳动物食性、杂食性、碎屑食性7个类群,其中浮游动物食性占渔获物重量组成的82.5%。春、秋季鱼类群落均主要由小型种类占优势,春季优势种有3种,为玉筋鱼(Ammodytes personatus)、鳀(Engraulis japonicus)和方氏锦鳚(Pholis fangi),秋季优势种有5种,分别是鳀、青鳞小沙丁鱼(Sardinella zunasi)、玉筋鱼、小黄鱼(Larimichthys polyactis)和赤鼻棱鳀(Thryssa kammalensis)。丰富度指数(D)、Shannon-Wiener多样性指数(H’)、均匀度指数(J’)的空间异质性明显,表现出近岸海域(尤其是青岛-乳山南部近岸海域)较高,深水区较低的态势,但多样性指数的季节间差异不显著。资源量与Shannon-Wiener多样性指数(H’)、均匀度指数(J’)、功能团多样性指数(FD)均呈负相关关系,与种类丰富度指数(D)则无相关关系。春、秋季鱼类群落长度谱曲线斜率均小于-0.2,而截距均大于10,与该海域1985年及2000年的研究结果相比,长度谱斜率显著降低、截距显著增加,这与小型个体种类占优势密切相关。与历史资料相比,黄海山东海域鱼类群落多样性下降,小型个体比例上升,资源呈衰退趋势。     

Incidence of heavy metals in the mangrove flora and sediments in Kerala, India

The mangroves of Kerala on the south-west coast of India are fast disappearing due to land reclamation and other anthropogenic disturbances. There are very few ecosystem level studies made in these much threatened biotopes in Kerala. The present study involves the measurement of heavy metals in the mangrove flora and sediments of three mangrove habitats along the Kerala coast. Sampling was carried out for a period of one year at bi-monthly intervals, with concentrations of Fe, Mn, Cu,Zn,Pb and Co analysed using atomic absorption spectrophotometry. An appreciable variation was observed in metal concentrations indifferent mangrove species. Cu, Zn and Pb were found to be in higher concentrations in Avicennia officinalis whereas higher levels of Fe, Mn and Co were observed in the species Barringtonia racemosa. The analysis of heavy metals indicated a high level of metal pollutants such as Fe, Cu, Zn and Pb in the mangrove habitats of Quilon and Veli compared to the relatively uncontaminated areas of Kumarakom. This revised version was published online in August 2006 with corrections to the Cover Date.     

新疆阿勒泰地区5个大赖草种群的表型多样性分析

为了解大赖草种群﹝Leymus racemosus ( Lam.) Tzvel.﹞的表型变异规律及多样性特征,对分布于新疆阿勒泰地区的5个大赖草种群(分别位于阿勒泰市、福海县、布尔津县和哈巴河县)的16个表型性状进行了测定;在此基础上,对各表型性状进行了Shannon-Weaver指数( H＇)分析和主成分分析。结果表明：各种群间的16个表型性状均存在较大差异,其中分布于哈巴河县的2个种群各表型性状的平均值均较高。种群内各表型性状的变异系数为5.97%~40.05%,差异较大;其中,穗下第一节间长度的变异系数在各种群内均较大(17.16%~40.05%);总体上看,种群内与营养生长有关的性状(如穗下第一节间长度、剑叶长度和宽度等)变异较大,而与繁殖有关的性状变异较小。在种群间,穗下第一节间长度、剑叶长度和宽度的变异系数均较大,分别为31.85%、26.87%和27.85%;而小穗和外颖长度以及穗节数的变异系数均较小,分别为15.21%、16.53%和16.91%。5个种群间16个表型性状的H＇值均有较大差异,并且,种群内各表型性状的H＇平均值(1.660)明显高于种群间(0.239)。主成分分析结果显示：前5个主成分的累计贡献率为80.210%,其中,第1主成分中与营养器官相关的性状(如株高、穗下第一节间长度、剑叶长度和宽度、茎节数)载荷较大,第2至第4主成分中与繁殖器官相关的性状(如穗长度和宽度、外颖和内颖长度、小穗长度和宽度以及外稃长度)载荷较大,表明这12个性状为大赖草种群表型性状变异的主要因子。研究结果显示：大赖草种群间的表型多样性低于种群内,且营养器官的表型变异是导致大赖草种群表型多样性的主要因子。     

Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea

The Changjiang estuary and the coastal area of the East China Sea (ECS) represent important interfaces of terrestrial and marine environments. This study included analyses of water and sediments collected during different seasons in these regions to determine the composition of microbial assemblages by means of 16S rRNA gene clone libraries. We retrieved 1946 sequences and 779 distinct operational taxonomic units from 36 clone libraries. Shannon–Weaver diversity index values and rarefaction analysis indicated that bacterial diversity in the sediment samples was much higher than in the water samples. Proteobacteria (72.9%) was the most abundant phylum, followed by Firmicutes (6.4%), Bacteroidetes (4.6%) and Actinobacteria (4.1%). In the water, clone sequences related to Alphaproteobacteria were the most abundant, whereas in the sediment samples, sequences affiliated with Gammaproteobacteria were predominant. Principal coordinate analysis showed that water samples collected from the Changjiang estuary and the ECS clustered separately. However, this spatial pattern could not be observed in sediment samples, which were mainly distinguished from one another by the season. Bacterial diversity in the Changjiang estuary was higher than that in the ECS, which may be the result of the mixing of bacterial communities from the Changjiang River, the estuary and the coastal ocean.     

Ethnic groups and biological diversity in medieval Spain: analysis of a Jew Necropolis from Sevilla

The skulls and mandibles of adults individuals from a Jewish necropolis of Sevilla (La Buhayra), (V–IX Cent. A.D.) have been analyzed. The results show that Sevillian Jews, both males and females, present narrow skulls with a notable dolichocrany. Sexual differences in both the height of the skull and the mandible robustness have been found. A comparison between Sevillian Jews and other Iberian samples from different epochs (Neolithic-Bronze to Centuries A.D.) has been carried out by means of a principal component analysis taken only into account the variability between groups. Results of the analysis showed a certain degree of biological differentiation between Sevillian and Catalonian Jews (XI–XIVth Centuries A.D.) which can be justified not only by the geographical distance and the temporal gap between the two groups, but also by the intrinsic heterogeneity of Jews (Nathan, 1961a, b; Nathan et al., 1963; Arensburg et al., 1980). The existence of some degree of biological variability between several ethnic-religious groups (Jew, Christians and Moslems) can be detected although they share a common Mediterranean background. Paper presented at the 4^th congress of the European Anthropology Association (Florence, Sept. 1984).     

Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China

The vertical distribution and diversity of sulfate-reducing prokaryotes (SRPs) in a sediment core from the Pearl River Estuary was reported for the first time. The profiles of methane and sulfate concentrations along the sediment core indicated processes of methane production/oxidation and sulfate reduction. Phospholipid fatty acids analysis suggested that sulfur-oxidizing bacteria (SOB) might be abundant in the upper layers, while SRPs might be distributed throughout the sediment core. Quantitative competitive-PCR analysis indicated that the ratios of SRPs to total bacteria in the sediment core varied from around 2–20%. Four dissimilatory sulfite reductase ( dsrAB) gene libraries were constructed and analyzed for the top layer (0–6 cm), middle layer (18–24 cm), bottom layer (44–50 cm) and the sulfate-methane transition zone (32–42 cm) sediments. Most of the retrieved dsrAB sequences (80.9%) had low sequence similarity with known SRP sequences and formed deeply branching dsrAB lineages. Meanwhile, bacterial 16S rRNA gene analysis revealed that members of the Proteobacteria were predominant in these sediments. Putative SRPs within Desulfobacteriaceae, Syntrophaceae and Desulfobulbaceae of Deltaproteobacteria , and putative SOB within Epsilonproteobacteria were detected by the 16S rRNA gene analysis. Results of this study suggested a variety of novel SRPs in the Pearl River Estuary sediments.     

Comparison of bacterial production in sediments, epiphyton and the pelagic zone of a lowland river

1. The microbial metabolism of organic matter in rivers has received little study compared with that of small streams. Therefore, we investigated the rate and location of bacterial production in a sixth‐order lowland river (Spree, Germany). To estimate the contribution of various habitats (sediments, epiphyton, and the pelagic zone) to total bacterial production, we quantified the contribution of these habitats to areal production by bacteria. 2. Large areas of the river bottom were characterized by loose and shifting sands of relatively homogenous particle size distribution. Aquatic macrophytes grew on 40% of the river bottom. Leaf areas of 2.8 m² m^?2 river bottom were found in a 6.6 km river stretch. 3. The epiphyton supported a bacterial production of 5–58 ng C cm^?2 h^?1. Bacterial production in the pelagic zone was 0.9–3.9 μg C L^?1 h^?1, and abundance was 4.0–7.8 × 10⁹ cells L^?1. Bacterial production in the uppermost 2 cm of sediments ranged from 1 to 8 μg C cm^?3 h^?1, and abundance from 0.84 to 6.7 × 10⁹ cells cm^?3. Bacteria were larger and more active in sediments than in the pelagic zone. 4. In spite of relatively low macrophyte abundance, areal production by bacteria in the pelagic zone was only slightly higher than in the epiphyton. Bacterial biomass in the uppermost 2 cm of sediments exceeded pelagic biomass by factors of 6–22, and sedimentary bacterial production was 17–35 times higher than in the overlying water column. 5. On a square meter basis, total bacterial production in the Spree was clearly higher than primary productivity. Thus, the lowland river Spree is a heterotrophic system with benthic processes dominating. Therefore, sedimentary and epiphytic bacterial productivity form important components of ecosystem carbon metabolism in rivers and shallow lakes. 6. The sediments are focal sites of microbial degradation of organic carbon in a sand‐bottomed lowland river. The presence of a lowland river section within a river continuum probably greatly changes the geochemical fluxes within the river network. This implies that current concepts of longitudinal biogeochemical relationships within river systems have to be revised.     

Microbial community composition and functional diversity in the rhizosphere of maize

This study investigates the small-scale stratification of bacterial community composition and functional diversity in the rhizosphere of maize. Maize seedlings were grown in a microcosm with a horizontal mesh (53 M) creating a planar root mat and rhizosphere soil. An unplanted microcosm served as control. Thin slices of soil were cut at different distances from the mesh surface (0.2–5.0 mm) and analysed for bacterial community composition by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16S rDNA and tested for activities of different enzymes involved in C, N, P and S cycling. Bacterial community composition and microbial functional diversity were affected by the presence of the maize roots. The bacterial composition showed a clear gradient up to 2.2 mm from the root surface, while no such gradient was observed in the unplanted pot. Invertase and phosphatase activities were higher in the close vicinity of maize roots (0.2–0.8 mm), whereas xylanase activity was unaffected. This study shows that the changes in bacterial community composition and functional diversity induced by roots may extend several millimetres into the soil.