Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods

Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this ‘environmental DNA’ (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey methods for targeted detection of single species, but few studies have investigated how well eDNA reflects whole communities of organisms in natural environments. We investigated whether eDNA can recover accurate qualitative and quantitative information about fish communities in large lakes, by comparison to the most comprehensive long‐term gill‐net data set available in the UK. Seventy‐eight 2L water samples were collected along depth profile transects, gill‐net sites and from the shoreline in three large, deep lakes (Windermere, Bassenthwaite Lake and Derwent Water) in the English Lake District. Water samples were assayed by eDNA metabarcoding of the mitochondrial 12S and cytochrome b regions. Fourteen of the 16 species historically recorded in Windermere were detected using eDNA, compared to four species in the most recent gill‐net survey, demonstrating eDNA is extremely sensitive for detecting species. A key question for biodiversity monitoring is whether eDNA can accurately estimate abundance. To test this, we used the number of sequence reads per species and the proportion of sampling sites in which a species was detected with eDNA (i.e. site occupancy) as proxies for abundance. eDNA abundance data consistently correlated with rank abundance estimates from established surveys. These results demonstrate that eDNA metabarcoding can describe fish communities in large lakes, both qualitatively and quantitatively, and has great potential as a complementary tool to established monitoring methods.     

Phosphorus release from resuspended sediment in the shallow and wind-exposed Lake Arresø, Denmark

Wind-induced sediment resuspension occurs frequently in the shallow and eutrophic Lake Arresø, Denmark. The impact of resuspension on internal phosphorus loading was investigated by laboratory experiments studying P-release from the undisturbed sediment surface and by experiments simulating resuspension events.Phosphorus release from undisturbed sediment sampled in May and August was 12 mg and 4 mg m^–2 d^–1, respectively. During experimental simulation of resuspension, soluble reactive phosphate (SRP) increased by 20–80 µg l^–1, which indicates that a typical resuspension event in the lake would be accompanied by the release of 150 mg SRP m^–2. The internal P loading induced by resuspension is estimated to be 60–70 mg m^–2 d^–1, or 20–30 times greater than the release from undisturbed sediment.SRP release during simulation of resuspension was mainly dependent on the equilibrium conditions in the water column and was basically independent of the increase in suspended solids and the duration of resuspension. A second simulation of resuspension conducted 26 hours later, did not result in any further release of SRP from sediment sampled in May. In contrast, there was an additional SRP release from sediment sampled in August, indicating that an exchangable P pool, capable of altering equilibrium conditions, is built up between resuspension events.It is concluded that resuspension, by increasing the P flux between sediment and water, plays a major role in the maintenance of the high nutrient level in Lake Arresø. A relatively high release rate is maintained during resuspension because of the low Fe:P ratio and the high concentration of NH₄Cl-extractable P in the sediment.     

Clear,crashing, turbid and back – long‐term changes in macrophyte assemblages in a shallow lake

相似文献   

青藏高原纳木错水生植物多样性及群落生态学研究

野外采集和文献记载结果显示纳木错共有水生植物34种(变种),隶属于15科19属。其中,轮藻门植物1科1属1种、单子叶植物7科8属16种、双子叶植物7科10属17种。纳木错区水生植物区系整体上表现出鲜明的北温带性质。种联结分析表明纳木错水生植物种间相关性显著,这些种组构成一个连续体。样地调查显示,纳木错主要水生植物群落有11种,以沉水植物群落类型为主,兼有少量的浮叶植物群落。β-多样性测度表明,样地间种类组成随水环境差异变化明显。       

Birgean heat budgets and rates of heat uptake in two monomictic lakes

Thermal profile development, rates of heat uptake and annual heat budgets are presented for two monomictic lakes, Whatcom and Washington, in the Puget Sound lowlands of Washington State. The rates of heat gain in the lakes were found to be significantly affected by lake morphometry. In turn, the differing rates of heat gain affected the annual heat budgets.     

新疆巴里坤、七角井和台特玛盐湖沉积物中免培养放线菌群落组成与离子成分分析

【背景】新型病原微生物层出不穷,放线菌作为最重要的抗生素生产菌仍受制于纯培养困难和菌种资源不足,而对于盐湖沉积物中的丰富放线菌资源却鲜有报道。【目的】探索巴里坤、七角井和台特玛盐湖沉积物放线菌群落结构及其多样性,分析盐湖沉积物中化学离子成分对放线菌群落的影响。【方法】每个盐湖采集5份样品并混合,使用SDS-CTAB抽提法提取总DNA,使用放线菌特异性引物进行PCR扩增并构建16S r RNA基因文库,每个样品随机挑选220个克隆子,经过Hae III酶切筛选后对阳性克隆子进行测序分析;对每个样品的8种主要化学离子进行检测,并将沉积物化学离子成分与放线菌群落进行关联性分析。【结果】获得的381个克隆序列属于143个操作分类单元(Operational taxonomic Unit,OTU),聚类结果显示从3个盐湖中共探测到37个放线菌属(台特玛盐湖:24;巴里坤盐湖:16;七角井盐湖:14)。3个盐湖共有的放线菌属为Aciditerrimonas、Aquihabitans、Demequina、Dietzia、Ilumatobacter和Amycolatopsis。从放线菌群落结构上看,台特玛盐湖与其他两湖差异性很大,巴里坤盐湖与七角井盐湖群落相似性更高,巴里坤、七角井和台特玛盐湖未知放线菌的组成分别为47.59%、53.07%和51.53%。利用RDA(Redundancy analysis)分析盐湖沉积物化学离子与放线菌群落的关联性,结果显示与Na~+、Cl~-和K~+相比,Mg~(2+)、Ca~(2+)、SO_4~(2-)、HCO_3~-和CO_3~(2-)与盐湖放线菌类群的相关关系要更加紧密。【结论】3个盐湖中具有丰富的放线菌多样性,包含大量的未知放线菌。盐湖沉积物不同的化学离子成分影响着各自独特的放线菌群落,可为开发新的盐湖放线菌资源提供依据。     

The dynamics of freshwater phytoplankton stability in the Naroch Lakes (Belarus)

The phytoplankton community of the Belarus Lakes Naroch, Myastro and Batorino, which have a Trophic State Index of 42.3, 60.7 and 66.8, respectively, underwent drastic changes to their structure during the period between 1968 and 2012. Thanks to an extensive monitoring program, these changes were well-documented and were qualitatively interpreted as signs of the community destabilization. The main objective of this study was the quantification of the ecological stability of the phytoplankton community in the Naroch Lakes. The approach to the quantification of ecological stability was based on defining the stability index as an inverse of the Euclidean Distance between the current and the reference states of the algal community (EuD-approach). The stability of the phytoplankton community was characterized by two indices: a “combined” index (SI[Comb]), and a “total community” index (SI[TotB]). SI[Comb] was calculated based on the individual taxonomic group biomasses and thus characterizes the stability of a community structure. SI[TotB] was calculated based on the values of the total algal biomass. Analyses of the results of this study extended the plausibility of the EuD-approach for the quantification of lake phytoplankton stability and allowed us to identify the dynamics of the stability of the Naroch Lakes phytoplankton. For the Naroch Lakes, we observed relatively larger SI[TotB] values in comparison with the SI[Comb] values. The results enabled us to examine the relationship between the lake trophic status and the stability of the phytoplankton community.     

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.     

Rhodospirillum sodomense,sp. nov., a Dead Sea rhodospirillum species

A new species of halophilic anoxygenic purple bacteria of the genus Rhodospirillum is described. The new organism, isolated from water/sediment of the Dead Sea, was vibrio-shaped and an obligate halophile. Growth was best at 12% NaCl, with only weak growth occurring at 6% or 21% NaCl. Growth occurred at Mg²⁺ concentrations up to 1 M but optimal growth was obtained at 0.05–0.1 M Mg²⁺. Bromide was well tolerated as an alternative anion to chloride. The new organism is an obligate phototroph, growing photoheterotrophically in media containing yeast extract and acetate or a few other organic compounds. Growth of the Dead Sea Rhodospirillum species under optimal culture conditions was slow (minimum t_d 20 h). Cells contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series and mass cultures were pink in color. Absorption spectra revealed the presence of a B875 (light-harvesting I) but no B800/B850 (light-harvesting II) photopigment complex. The new organism shares a number of properties with the previously described halophilic phototrophic bacterium Rhodospirillum salinarum and was shown to be related to this phototroph by 16S rRNA sequencing. However, because of its salinity requirements, photosynthetic properties, and isolation from the Dead Sea, the new phototroph is proposed as a new species of the genus Rhodospirillum, R. sodomense.     

Exploration of Ellsworth Subglacial Lake: a concept paper on the development, organisation and execution of an experiment to explore, measure and sample the environment of a West Antarctic subglacial lake

Antarctic subglacial lakes have, over the past few years, been hypothesised to house unique forms of life and hold detailed sedimentary records of past climate change. Testing this hypothesis requires in situ examinations. The direct measurement of subglacial lakes has been considered ever since the largest and best-known lake, named Lake Vostok, was identified as having a deep water-column. The Subglacial Antarctic Lake Environments (SALE) programme, set up by the Scientific Committee on Antarctic Research (SCAR) to oversee subglacial lakes research, state that prior exploration of smaller lakes would be a “prudent way forward”. Over 145 subglacial lakes are known to exist in Antarctica, but one lake in West Antarctica, officially named Ellsworth Subglacial Lake (referred to hereafter as Lake Ellsworth), stands out as a candidate for early exploration. A consortium of over 20 scientists from seven countries and 14 institutions has been assembled to plan the exploration of Lake Ellsworth. An eight-year programme is envisaged: 3 years for a geophysical survey, 2 years for equipment development and testing, 1 year for field planning and operation, and 2 years for sample analysis and data interpretation. The science experiment is simple in concept but complex in execution. Lake Ellsworth will be accessed using hot water drilling. Once lake access is achieved, a probe will be lowered down the borehole and into the lake. The probe will contain a series of instruments to measure biological, chemical and physical characteristics of the lake water and sediments, and will utilise a tether to the ice surface through which power, communication and data will be transmitted. The probe will pass through the water column to the lake floor. The probe will then be pulled up and out of the lake, measuring its environment continually as this is done. Once at the ice surface, any water samples collected will be taken from the probe for laboratory analysis (to take place over subsequent years). The duration of the science mission, from deployment of the probe to its retrieval, is likely to take between 24 and 36 h. Measurements to be taken by the probe will provide data about the following: depth, pressure, conductivity and temperature; pH levels; biomolecules (using life marker chips); anions (using a chemical analyzer); visualisation of the environment (using cameras and light sources); dissolved gases (using chromatography); and morphology of the lake floor and sediment structures (using sonar). After the probe has been retrieved, a sediment corer may be dropped into the lake to recover material from the lake floor. Finally, if time permits, a thermistor string may be left in the lake water to take time-dependent measurements of the lake’s water column over subsequent years. Given that the comprehensive geophysical survey of the lake will take place in two seasons during 2007–2009, a two-year instrument and logistic development phase from 2008 (after the lake’s bathymetry has been assessed) makes it possible that the exploration of Lake Ellsworth could take place at the beginning of the next decade.