Response of Archaeal Community Structure to Environmental Changes in Lakes on the Tibetan Plateau,Northwestern China

To study how archaeal community responds to environmental changes, we investigated archaeal community structures in waters of three Tibetan saline lakes in northwestern China (Gahai, Xiaochaidan, and Charhan Lakes) with 16S rRNA gene phylogenetic analysis. Temperature, pH, and water chemistry (major anions and cations) of the lakes were measured. Three archaeal clone libraries were constructed with a total of 297 sequences. Incorporating our previous data obtained from other lakes on the Tibetan Plateau, we performed statistical analyses to identify dominant environmental parameters that could account for the observed variations in archaeal community structure. We concluded that salinity and water chemistry (Na and bicarbonate concentration in particular) played an important role in shaping archaeal community. In particular, the relative abundance of archaeal 16S rRNA genes affiliated with the Halobacteriales of the Euryarchaeota increased with salinity, whereas that of crenarchaeotal 16S rRNA gene sequences showed the opposite trend. Crenarchaeotal 16S rRNA gene sequences were retrieved from lake waters with salinity up to 28.3%. These results have important implications for our understanding of response of archaeal community to environmental changes in high-altitude lake ecosystems.     

The Distribution of Mercury in the Sediments of Eight Saskatchewan Lakes

Eight lakes located in the southern half of Saskatchewan were sampled in May and June, 1987, to determine the concentration and spatial distribution of mercury in their surface sediments. Katepwa and Buffalo Pound lakes had maximum total mercury sediment concentrations of 0.158 and 0.100 μg · g⁻¹ dry weight respectively, while in the other six lakes the mercury concentration was never greater than 0.04 μg · g⁻¹ dw. Despite this difference in mercury concentration in the sediments of the lakes, walleye sampled from them have high mercury concentrations exceeding 0.5 μ · g⁻¹ (wet weight).     

Structure Distinctions of Pelagic Rotifer Plankton in Stratified Lakes With Different Human Impact

Pelagic rotifer plankton was studied in four stratified lakes with different degrees of human impact from June to July 2001 and throughout 2002. Rotifer species diversity was closely correlated to temperature and oxygen concentration (correlation coefficients were 0.90 and 0.87, respectively) in the water column of the hypertrophic Lake Kruglik. In the mesotrophic lakes, the correlation coefficients were much lower and their reduction was related to decreasing human impact on the lakes. Species richness was similar in Lakes Kruglik and S. Volos, but the spatial structure of the community differed greatly. The maximum rotifer density was observed in the epilimnion of Lake Kruglik, with densities dropping sharply towards the hypolimnion. In the mesotrophic lakes, the highest rotifer density was recorded in the meta- and hypolimnion. A comparative analysis of the morphometric characteristics of Keratella cochlearis showed that (1)␣the lorica length of ovigerous females increased in all four lakes with decreasing temperature; (2) the shortest lorica length was in Lake Kruglik at the same temperature; (3) in the mesotrophic lakes a significant increase in lorica length occurred as the temperature decreased from 14.2 °C to 4.2 °C. There is the similar relationship in rotifers of the genus Filinia. Hypoxia in the clino- and hypolimnion of Lake Kruglik reduced the diversity of spatial niches created by thermal stratification. As a result, the number of non-overlapping niches for rotifers in Lake Kruglik is reduced by a factor of 2–5 compared to that in mesotrophic lakes, but the mean value of the overlapping index is significantly higher.     

Abundance and Diversity of Sulfur-Oxidizing Bacteria along a Salinity Gradient in Four Qinghai-Tibetan Lakes,China

Sulfur-oxidizing bacteria (SOB) play important roles in the sulfur cycle and are widespread in a number of environments, but their occurrence and relationship to geochemical conditions in (hyper)saline lakes are still poorly understood. In this study, the abundance and diversity of SOB populations were investigated in four Qinghai-Tibetan lakes (Erhai Lake, Gahai Lake 1, Gahai Lake 2 and Xiaochaidan Lake) by using quantitative polymerase chain reaction (qPCR) and soxB gene- (encoding sulfate thiohydrolase) based phylogenectic analyses. qPCR analyses showed that in the studied lakes, the total bacterial 16S rRNA and soxB gene abundances in the sediments were distinctly higher than in the overlying waters. The 16S rRNA gene abundance in the waters ranged 5.27 × 10⁶–6.09 × 10⁸ copies per mL and 7.39 × 10¹⁰–2.9 × 10¹¹ copies per gram sediment. The soxB gene abundance in the waters ranged from 1.88 × 10⁴ to 5.21 × 10⁵ per mL and 4.73 × 10⁶–2.65 × 10⁷ copies per gram sediment. The soxB gene in the waters of the two hypersaline lakes (Gahai Lake 2 and Xiaochaidan Lake) was more abundant (2.97 × 10⁵ and 5.21 × 10⁵ copies per mL) than that in the two low-salinity lakes (1.88 × 10⁴ and 3.36 × 10⁴ copies per mL). Phylogenetic analysis showed that Alpha- and Betaproteobacteria were dominant SOB in the investigated lakes, and the composition of proteobacterial subgroups varied with salinity: in freshwater Erhai Lake and low-salinity Gahai Lake 1, the SOB populations were dominated by the Betaproteobacteria, whereas in hypersaline Lake Gahai 2 and Xiaochaidan Lake, the SOB populations were dominated by Alphaproteobacteria. Overall, salinity played a key role in controlling the diversity and distribution of SOB populations in the investigated Qinghai-Tibetan lakes.     

滇中高原湖泊鱼类多样性的研究

依据历年馆藏的鱼类标本和资料,采用多元逐步回归与多项式逐步回归的分析方法,系统分析了滇中6个高原湖泊鱼类的物种丰度、特有种以及属的数目与7个主要湖泊环境因子之间的关系。分析结果显示,控制湖泊鱼类物种丰度、特有种数和属数的关键湖泊环境因子是湖泊面积和湖岸线长度;其中与湖泊面积呈显著正相关,而与湖岸线长度呈负相关。分析不停留于这一常规的横向比较,而是从历史生物地理学的角度,更深入一步揭示了滇中6个湖泊鱼类多样性的演化实质上是受湖泊的发育阶段所控制的。     

Analysis of Methanogenic Archaeal and Sulphate Reducing Bacterial Populations in Deep Sediments of the Black Sea

In this study, the distribution, morphology and relative abundance of Sulfate Reducing Bacterial (SRB) and Methanogenic Archaeal (MA) populations in the Black Sea sediments were investigated by using in situ hybridization with fluorescently labeled rRNA-targeted oligonucleotide probes. Results were discussed with respect to the characteristics of sampling points. MA and SRB showed a great diversity in all sediment samples. Higher abundance of MA (20–30%) and SRB (30–35%) populations were observed within the sediments from deeper parts of the Black Sea than the shallower parts (10–11% MA and 13–14% SRB). Desulfobotulus, Desulfosarcina and Desulfococcus groups were the most commonly detected SRB groups in the Black Sea sediments. Relative percentage of these SRB groups within sediments from deeper parts of the Black Sea was in a range of 17–21% whereas that of was in a range of 4–5% within the sediments from the shallower parts. Order Methanococcales were the dominant methanogenic group in all samples. Relative percentages of order Methanococcales were in a range of 8–12% and 4–5% within sediments from deeper parts and the coastal parts of the Black Sea, respectively.     

Bacterial and Archaeal Community Structure in the Surface Diatom Sediments of Deep Freshwater Lake Baikal (Eastern Siberia)

Diatom sediment records of large lakes can be used to decipher the history of ancient phytoplankton. The upper layer of the sediment is an important area of remineralization of the sedimenting phytoplankton biomass. It hosts a bacterial community different from those of both the water column and deeper sediment layers. In this work, we analyzed the structure and diversity of the communities of Bacteria and Archaea in the surface sediment core containing valves of diatoms, the major producers in Lake Baikal. Pyrosequencing of the bacterial V3–V4 region of the 16 S ribosomal RNA (rRNA) and archaeal V1–V3 16 S rRNA gene regions yielded 29,168 and 36,997 reads, respectively. In total, we have identified 33 bacterial phyla; uncultured Actinobacteria were the most abundant in the upper layers, while lower sediment was dominated by Firmicutes and Alphaproteobacteria. The composition of the archaeal community changed with depth, but was generally dominated by Crenarchaeota from the classes Marine Group I and Miscellaneous Crenarchaeotic Group, as well as Euryarchaeota from the class Thermoplasmata. These dominant bacterial and archaeal taxa are presumed to participate in the destruction of buried organic matter, which eventually leads to degradation of the diatom valves.     

A Quantitative Study of the Comparative Distribution of Non-parasitic Leeches and Triclads in the Stony Littoral of British Lakes

For each of the three species of leeches and four species of triclads inhabiting the stony littoral of 100 British lakes of diverse trophic status, numbers, biomass and mean weight were correlated against a wide range of physical, chemical and other variables. Very few significant correlations were found between the various biological variables and the non-chemical variables. Significant, positive correlations were obtained for all leech and triclad variables against all of the chemicals, with the exception of Erpobdella octoculata numbers, Helobdella stagnalis mean weight and all of the Polycelis nigra variables which did not correlate with any. Relationships between biological variables and calcium content are given special consideration. Over the range of lakes investigated, total triclad numbers exceeded leech numbers but the reverse was usually true for total biomass. Correlations between the various leech and triclad variables are examined.     

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes

We have developed a machine-learning approach to identify 3537 discrete orthologue protein sequence groups distributed across all available archaeal genomes. We show that treating these orthologue groups as binary detection/non-detection data is sufficient to capture the majority of archaeal phylogeny. We subsequently use the sequence data from these groups to infer a method and substitution-model-independent phylogeny. By holding this phylogeny constrained and interrogating the intersection of this large dataset with both the Eukarya and the Bacteria using Bayesian and maximum-likelihood approaches, we propose and provide evidence for a methanogenic origin of the Archaea. By the same criteria, we also provide evidence in support of an origin for Eukarya either within or as sisters to the Thaumarchaea.     

Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea

The continental shelf and slope in the northern South China Sea is well known for its prospect of oil/gas/gas-hydrate resources. To study microbial communities and their roles in carbon cycling, a 4.9-m sediment core was collected from the Qiongdongnan Basin on the continental slope of the South China Sea during our cruise HY4-2005-5 in 2005. Geochemical, mineralogical, and molecular phylogenetic analyses were carried out. Sulfate concentration in pore water decreased with depth. Abundant authigenic carbonates and pyrite were observed in the sediments. The bacterial community was dominated by aerobic and facultative organisms. Bacterial clone sequences belonged to the Gamma-, Alpha-, Deltaproteobacteria and Firmicutes group, and they were related to Fe(III) and/or Mn(IV) reducers, sulfate reducers, aromatic hydrocarbon degraders, thiosulfate/sulfite oxidizers, and denitrifiers. Archaeal clone sequences exhibited greater overall diversity than the bacterial clones with most sequences related to Deep-Sea Archaeal Group (DSAG), Miscellaneous Crenarchaeotic Group (MCG), and Uncultured Euryarchaeotic Clusters (UECs). Archaeal sequences related to Methanosarcinales, South African Gold Mine Euryarchaeotic Group (SAGMEG), Marine Benthic Group-D (MBG-D) were also present. Most of these groups are commonly present in deep-sea sediments, particularly in methane/organic-rich or putative methane hydrate-bearing sediments.     

长江中下游湖泊贝类物种濒危状况评估

长江中下游是我国淡水贝类资源分布最为集中的地区.由于人类活动加剧,该区域贝类受到严重威胁.为系统评估贝类物种现状,于2003年5月至2005年6月对13个典型湖泊进行了系统调查.共采集贝类69种,其中中国特有种44种.不同类型湖泊贝类的组成差别较大.通江湖泊的物种明显较丰富,尤其是适应流水生境的种类,如河螺属、短沟蜷属及蚌科的种类.大型通江湖泊鄱阳湖和洞庭湖的贝类分别有53种和57种,占总数的76.8%和82.6%.阻隔湖泊的物种较少,在4-19种之间.对67种贝类濒危等级的评价结果表明,近危及受威胁的种类占58.2%,只有37.3%的种类种群稳定.与历史资料相比,该区域贝类的多样性已明显下降,双壳类优势类群由大型的蚌类演变为小型的河蚬.分析显示,贝类资源衰退的主要原因是江湖阻隔、过度捕捞和水体污染等人为干扰.     

An Analysis of Fish Species Richness in Natural Lakes

There is a growing recognition of the need to conserve biodiversity that has been conceptualised in the Convention of Biological Diversity. Maintenance of fish species richness is particularly important, because habitat degradation in inland waters continues to accelerate on a global scale. Here we develop empirical models for predicting fish species richness in natural lakes in various geographical regions of the world. In tropical lakes where fish biodiversity is richer than in temperate lakes, fish species richness can be predicted by a few variables such as lake area and altitude. Low fish species richness in most temperate lakes might be due to the effect of glaciation on colonisation and speciation of fishes. In US, Canadian and northern European lakes, lake acidification is one of the important factors influencing fish species richness. Although limnological characteristics influence fish species richness in temperate lakes, lake area and altitude have greater predictive power. This is in contrast to fish species richness in rivers, which can be reliably predicted by basin area. In the power curves, which describe the relationship between fish species richness and habitat size in lakes and rivers, the exponent is always greater in tropical regions than in temperate regions. Because fish biodiversity is greater in the tropics threats to fish biodiversity through habitat degradation are greater than those in temperate inland waters.     

The Stone Brusher, a New Sampler for Submerged Epilithic Material in Shallow Streams and Lakes

The Stone Brusher is designed to take qualitative or semi-quantitative samples of material attached to stones at 7–50 cm depth in running or stagnant waters. The epilithic material is dislodged from the stone surface with a rotating brush enclosed in a chamber and the material is drawn up directly into the sample bottle with an air-cylinder. The operator takes a sample quickly and without putting hands into the water. The sampling area is about 28 cm². The sampler is made of plastic, stainless steel and aluminium and weighs 3.1 kg. The equipment is robust and easily handled and it is constructed to meet the demand for standardized sampling for research and environmental monitoring and to improve working conditions for sampling personnel. The equipment allows sampling from bedrock and large stones that cannot be lifted from the bottom and it can be used for reliable sampling also in fast-flowing streams where the dislodged material is easily flushed away. Using Near-Infrared Spectroscopy and diatom analyses, this new sampler is evaluated in comparison to the recognized toothbrush method, which indicates that the Stone Brusher reduces sampling variability compared with the toothbrush method.     

Archaeal Diversity and Spatial Distribution in the Surface Sediment of the South China Sea

Archaea represent a significant portion of biomass in the marine sediments and may play an important role in global carbon cycle. However, the identity and composition of deep sea sediment Archaea are unclear. Here, we used the archaeal 16S rRNA gene primers to determine the diversity and community structure of Archaea from shallow water (<100 m) and deep water (>1500 m) sediments in the South China Sea. Phylogenetically the archaeal community is separated between the shallow- and deep sea sediments, with the former being dominated by the Thaumarchaeota and the latter by the Marine Benthic Group B, E and the South African GoldMine Euryarchaeotal Group as well as Thaumarchaeota. Sand content showed significant correlation with Thaumarchaeota, suggesting that the porous media may create an oxic environment that allowed these aerobic organisms to thrive in the surface sediments. The carbon isotope composition of total organic carbon was significantly correlated to the distribution of archaeal groups, suggesting that Archaea overall may be constrained by the availability or sources of organic carbon in the sediments of the South China Sea.     

Lakes as nitrous oxide sources in the boreal landscape

Estimates of regional and global freshwater N₂O emissions have remained inaccurate due to scarce data and complexity of the multiple processes driving N₂O fluxes the focus predominantly being on summer time measurements from emission hot spots, agricultural streams. Here, we present four‐season data of N₂O concentrations in the water columns of randomly selected boreal lakes covering a large variation in latitude, lake type, area, depth, water chemistry, and land use cover. Nitrate was the key driver for N₂O dynamics, explaining as much as 78% of the variation of the seasonal mean N₂O concentrations across all lakes. Nitrate concentrations varied among seasons being highest in winter and lowest in summer. Of the surface water samples, 71% were oversaturated with N₂O relative to the atmosphere. Largest oversaturation was measured in winter and lowest in summer stressing the importance to include full year N₂O measurements in annual emission estimates. Including winter data resulted in fourfold annual N₂O emission estimates compared to summer only measurements. Nutrient‐rich calcareous and large humic lakes had the highest annual N₂O emissions. Our emission estimates for Finnish and boreal lakes are 0.6 and 29 Gg N₂O‐N/year, respectively. The global warming potential of N₂O from lakes cannot be neglected in the boreal landscape, being 35% of that of diffusive CH₄ emission in Finnish lakes.     

Salinity as a determinant of the structure of biological communities in salt lakes

The paper considers the extent to which salinity determines the structure of biological communities (composition and species richness and diversity) in saline lakes, i.e. inland bodies of water with salinities in excess of 3 g l-1. It also considers the extent to which oxygen, ionic composition, pH, hydrological patterns (degree of permanence and impermanence of water), geographical position, palaeoclimatic events, chance, human intervention, and biological interactions especially predation determine biological communities in salt lakes. It suggests that salinity is less significant as a determinant of community structure in salt lakes than has been assumed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Biological and ecological features of saline lakes in northern Tibet,China

In May and July 2001, the biological and ecological features of 22 salt lakes in northern Tibet , China, were investigated.Their salinity ranged from 1 to 390 g l^–1. One hundred and thirty two samples were collected. Ninty five taxa of phytoplankton and 42 taxa of zooplankton were recorded. The dominant cation was sodium, with magnesium generally sub-dominant; CO₃^2– was the dominant anion in low salinity, chloride was the dominant anion with increasing salinity. Major species were Gloeothece linearis, Oscillatoria tenuis, Chroococcus minutus (blue-green algae); Navicula spp, Cymbella pusilla, Diatoma elongatum(diatoms); Dunaliella salina, Chlorella vulgarisand Ulothrix tenerrima (green algae). Major zooplankton included: Vorticella campanula, Epistylis daphniae (Protista); Keratella quadrata, Brachionus plicatilis (Rotifera); Artemiaspp. (Anostraca); Daphniopsis tibetana (Cladocera); Cletocamptus dertersiand Cyclops vicinus (Copepoda). Ten species were recorded in hypersaline waters; apart from those metioned above, they included CyclidiumsppLitonotus fasciola, Euplotes terricola, Strombilidium viride, Brachionus variabilis, Colurella adriatica, Keratella cochlearis, Colurella adriatica, and Cyclops sp. Seven taxa of benthic macroinvertebrates are recorded, represented by Cyprissp. (Ostracoda), Gammarus sp. (Amphipoda), Radixsp. and Hippeutis sp. (Mollusca); chiroonomids Tendipus group salinarius (Diptera), Nematoda, Trochophora and Ephrdra sp. At present, there are fishes only in Bangong Co., and no fishes recorded in other salt lakes. The total number of plankton species has a significantly negative correlation with the salinity, and decreased with increasing altitude, but not significant.     

环境和扩散对草地群落构建的影响

植物群落构建机制是生态学研究的热点之一.长久以来这个难题并没有得到很好的解释,且争议较多.生态位理论或中性理论,或是二者的共同作用,这样的结论在不同的研究中都有印证.以黄土高原子午岭地区的草地群落为例,对3种不同的草地群落(5a的弃耕地、阴坡和阳坡的草地)进行了野外群落学调查,采用Mantel test和主轴邻距法(PCNM)分析方法,研究了空间地理距离和环境资源差异对于草本植物群落分布的影响,结果表明:地理距离和环境差异共同解释了群落组成相似性的79.3％,剔除环境因子的影响,地理距离解释了群落组成相似性的33.8％;而剔除地理距离的影响,环境因子解释了群落组成相似性的14.2％.无论是生态位理论还是中性理论,其在黄土高原草本群落构建过程中都有作用,但中性理论扮演了更为重要的角色.     

Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea

To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea (SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S rRNA and 16S rRNA gene (V1‐3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S rRNA vs. rDNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance‐decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay.