Estimating species richness using environmental DNA

The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion‐based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.     

Seed reproductive biology of the rare aquatic carnivorous plant Aldrovanda vesiculosa (Droseraceae)

Despite the unprecedented global decline in extant populations of Aldrovanda vesiculosa in the last century, little is known about the reproductive biology of this iconic aquatic carnivorous plant. This study aimed to investigate the role of seed‐based reproduction in the ecology of A. vesiculosa, with particular focus on the interplay between the regulation of seed dormancy by temperature cues and the efficacy of exogenous ethylene gas to act as a germination stimulant, the desiccation capacity and long‐term storage potential of seeds for conservation purposes. Sexual reproduction appears to be extremely limited in both natural and naturalized populations across three continents, with high variability in the success of flowering and seed set between sites and between seasons. Overall, flowering yielded few fertile fruit (6–19% of flowers producing fertile fruit) and seed viability was variable but generally low (29–88%). Fecundity appears to be influenced by seasonal climatic conditions and microhabitat characteristics. Aldrovanda vesiculosa possesses physiologically dormant seeds, with germination stimulated by exposure to ethylene gas (>90% germination) at 25 °C. Seeds appear sensitive to desiccation and sub‐zero temperature storage, with no germination and markedly reduced embryo growth after storage of seeds for >1 month at 15 °C and 15% relative humidity or after short‐term (24 h) storage at ?18 °C. In the absence of significant conservation and restoration initiatives, the continuing decline of dystrophic freshwater wetland habitats globally leaves A. vesiculosa facing extinction. As the successful long‐term storage of seeds appears unfeasible based on the approaches described in this study, other alternatives for germplasm conservation such as cryostorage of vegetative tissues or zygotic embryos must be considered for establishing long‐term ex situ collections of critical germplasm.     

A multi‐basin approach determines variability in host fish suitability for unionids in tributaries of the Laurentian Great Lakes

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Phosphorus accumulates faster than nitrogen globally in freshwater ecosystems under anthropogenic impacts

Combined effects of cumulative nutrient inputs and biogeochemical processes that occur in freshwater under anthropogenic eutrophication could lead to myriad shifts in nitrogen (N):phosphorus (P) stoichiometry in global freshwater ecosystems, but this is not yet well‐assessed. Here we evaluated the characteristics of N and P stoichiometries in bodies of freshwater and their herbaceous macrophytes across human‐impact levels, regions and periods. Freshwater and its macrophytes had higher N and P concentrations and lower N : P ratios in heavily than lightly human‐impacted environments, further evidenced by spatiotemporal comparisons across eutrophication gradients. N and P concentrations in freshwater ecosystems were positively correlated and N : P was negatively correlated with population density in China. These results indicate a faster accumulation of P than N in human‐impacted freshwater ecosystems, which could have large effects on the trophic webs and biogeochemical cycles of estuaries and coastal areas by freshwater loadings, and reinforce the importance of rehabilitating these ecosystems.     

Strong invaders are strong defenders – implications for the resistance of invaded communities

Many ecosystems receive a steady stream of non‐native species. How biotic resistance develops over time in these ecosystems will depend on how established invaders contribute to subsequent resistance. If invasion success and defence capacity (i.e. contribution to resistance) are correlated, then community resistance should increase as species accumulate. If successful invaders also cause most impact (through replacing native species with low defence capacity) then the effect will be even stronger. If successful invaders instead have weak defence capacity or even facilitative attributes, then resistance should decrease with time, as proposed by the invasional meltdown hypothesis. We analysed 1157 introductions of freshwater fish in Swedish lakes and found that species’ invasion success was positively correlated with their defence capacity and impact, suggesting that these communities will develop stronger resistance over time. These insights can be used to identify scenarios where invading species are expected to cause large impact.     

Field evaluation of oxygen consumption by two freshwater decapod morphotypes (Trichodactylidae and Aeglidae); the effect of different times of the day,body weight and sex

We report an analysis of the effect of two different times of day (noon and dusk), body weight and sex on the oxygen consumption rate (OCR) of the freshwater crabs Trichodactylus kensleyi (Trichodactylidae), Aegla singularis and A. platensis (Aeglidae) in their natural environment. Both families are sympatric in the studied locations, with a co-occurrence found between T. kensleyi and A. singularis or T. kensleyi and A. platensis. The mean OCR was highest in A. singularis and lowest in A. platensis. The OCR was higher in Aegla species at noon, and Trichodactylus consumed more oxygen at dusk. In aeglids, there was no difference in oxygen consumption between noon and dusk. T. kensleyi exhibited statistically significant differences in the OCR between noon and dusk. The oxygen uptake of all three species analysed was not influenced by the sex of the individual but varied according to the animals’ weight. The families evaluated share some biological and ecological characteristics, such as diet and habitats, but the strategies used in the regulation of gas exchange at different times of the day were different. Environmental factors may be influencing the oxygen consumption of each morphotype differently.     

毛筒壳科真菌次级代谢产物生物活性的评价

毛筒壳科Tubeufiaceae真菌具有产新结构、新活性次级代谢产物的潜力,目前对该科真菌次级代谢产物的研究较少。为了寻找具有生物活性的新化合物,有必要对毛筒壳科真菌次级代谢产物及其活性进行系统深入的研究。本文采用平板对峙法、生长速率法和MTT法,分别测定已分离得到的19株该科真菌活体菌株抑菌活性、发酵物抑菌活性以及发酵物粗提物对不同人体肿瘤细胞株增殖的抑制作用。通过平板对峙法,试验共筛选获得13株活性菌株,其中,红棕毛筒腔菌菌株Tubeufia rubra PF02-2对7种植物病原真菌有明显的抑菌效果,抑制率均高于60%且抑菌谱广。采用生长速率法,发现红棕毛筒腔菌菌株PF02-2经液体发酵后,发酵液对其中4种植物病原真菌仍有一定的抑制作用,且菌丝体部分的乙酸乙酯提取物对马铃薯早疫病病菌Alternaria solani（ZYB）的抑制效果最好。通过MTT法,发现发酵物粗提物对3种肿瘤细胞均具有不同程度的细胞毒活性,其中在300μg/mL时,剑叶莎毛筒腔菌菌株Tubeufia machaerinae ML03-2发酵液部分的乙酸乙酯提取物对人宫颈癌细胞株HeLa和人前列腺癌细胞株PC-3的抑制率（%）分别达到了98.92±0.15和97.86±0.18,在400μg/mL时,对人肝癌细胞株HEPG2的抑制率（%）达到了98.88±0.04;在500μg/mL时,明孢新旋卷孢菌菌株Neohelicosporium hyalosporum ML05-1菌丝体部分的乙酸乙酯提取物对人宫颈癌细胞株HeLa细胞的抑制率（%）为98.32±0.02,在600μg/mL时,对人肝癌细胞株HEPG2的抑制率（%）达到了97.62±0.20,在300μg/mL时,对人前列腺癌细胞株PC-3的抑制率（%）达到了98.91±0.02。该研究结果为开发利用毛筒壳科真菌提供了科学依据。     

Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

DNA metabarcoding can contribute to improving cost‐effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time‐consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column‐based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic‐based enzymatic protocol (BEAD), and a 313‐bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7–14 than 1–7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.     

滇西北高山微水体与溪流生境底栖动物多样性和环境特征

高山微水体由于面积微小且通过地表径流形成串联结构常常被认为与高山溪流具有类似的生境, 然而由于这两类生境中环境因子与底栖动物多样性存在差异, 它们在生态系统中的作用可能完全不同。滇西北地区是全球生物多样性热点区域之一, 境内高山微水体和高山溪流分布密集, 在区域底栖生物多样性维持方面具有重要的功能, 然而目前对这两类高山淡水生态系统的研究较少。为了比较这两类生境环境因子的异同及其对底栖动物多样性的维持作用, 2015年6月, 作者在云南省怒江州贡山县的高山峡谷内, 对27个高山微水体和同区域分布的1条高山溪流(海拔高差500 m范围)的底栖动物多样性和水环境因子进行了实地调查。结果表明: (1)高山微水体和高山溪流底栖动物群落中优势分类单元种群数量均比较庞大, 而稀有分类单元数量较多且种群较小; (2)两种生境在环境因子、物种多样性、功能多样性和群落结构方面的差异明显, 高山溪流有较高的物种丰富度、物种多样性和功能多样性; (3)高山微水体底栖动物多样性的分布与水环境因子无关, 而高山溪流底栖动物多样性与群落结构的形成受到与流速关联的水环境因子和海拔的影响。因此, 高山微水体与高山溪流不能简单地视为类似的生境类型, 它们对区域底栖动物多样性和生态功能维持可能具有不同的作用。     

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River

Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin using 4,434 nuclear loci, and tested the history of freshwater invasion of C. nasus. We found that both C. brachygnathus and C. nasus were valid species, but the resident C. nasus taihuensis and the anadromous C. nasus were not different genetically based on Bayes factor species delimitation (BFD*). Maximum likelihood tree, Network, PCA and STRUCTURE analyses all corroborated the results of BFD*. Two independent freshwater invasion events of C. nasus were supported, with the first event occurring around 4.07 Ma and the second happened around 3.2 Ka. The time of the two freshwater invasions is consistent with different paleogeographic events. Estimation showed that gene flow was higher within ecotypes than between different ecotypes. F‐DIST analyses identified 120 disruptive outliers by comparing C. brachygnathus to anadromous C. nasus, and 21 disruptive outliers by comparing resident C. nasus to anadromous C. nasus. Nine outliers were found to be common between the two comparisons, indicating that independent freshwater invasion of C. nasus might involve similar molecular pathways. The results of this study suggest that adaptation to landlocked freshwater environment of migratory fish can evolve multiple times independently, and morphology of landlocked ecotypes may cause confusion in their taxonomy.